Storyline III

Abduction
The story begins with the Illusive Man aboard his secret space station, orbiting a star that is near the end of its life. The Illusive Man receives a transmission from Kai Leng, Cerberus' top "wet-work" agent. In the transmission, Leng details how he located Paul Grayson, a former Cerberus Operative who betrayed them three years ago during the events of Mass Effect: Ascension, on the lawless Omega space station in the Terminus Systems. The Illusive Man is pleased by the news and tells Leng to capture Grayson alive, for he needs human subjects for his investigation into Reaper technology recovered from the Collector Base.

Grayson is currently working for Aria, the so-called "pirate queen" of Omega. He along with his batarian partner Sanak, and an asari named Liselle, are at a warehouse completing a job given to them by Aria. They take out their turian targets quickly, who are part of a gang on Omega called the Talons, who have recently not been paying Aria her cut from their drug dealing operation. They snatch the large quantity of red sand, a potent drug that gives humans a very large high, from the Talon warehouse and leave. They stash the red sand at Grayson's apartment, since they do not want to bring it into the Afterlife Club. Sanak and Liselle leave his apartment with Grayson staying behind momentarily, stating he will catch up to them soon. He opens up a comm channel with Kahlee Sanders, who is currently at the Jon Grissom Academy for the Ascension Project, and asks her how everything is going with his daughter, which he did about once a month. She is glad to talk to him again but slightly put on edge from his sloppy appearance, since it had changed so much since their last talk. Grayson is also put on edge by the conversation, though it is revealed that he is always on edge after their calls. After their call ended, Grayson is tempted by all the red sand in his apartment, but fought the urge, saying repeatedly to himself that he had been clean for years for his daughter's sake. He leaves his apartment and heads over to Afterlife, where he meets up with Aria as she is scolding the Talons for not paying her and saying that taking out their warehouse was only retribution. She 'negotiated' an increase in the required cut she would receive from their drug dealing. The Talons grudgingly accepted her new terms and left.

The Talons are not the only problem Grayson has to deal with on Omega though, as Kai Leng has been watching him for days, and has planned out his kidnap attempt. Seeing Grayson leave Afterlife alone sets his plan into motion – he and five other Cerberus operatives begin their strike. They manage to get into Grayson's apartment complex under the guise of going to Grayson's birthday party, even bringing presents along. Each of them brings a concealed tranquilliser gun, since killing Grayson was not part of the plan. However, unknown to them, Grayson had invited Liselle over to his apartment since he was too tempted by the red sand, and needs to 'replace one addiction with another' - as he and Liselle have been sleeping together for some time. The Cerberus operatives hack the door, and assault his apartment. After a struggle ensues, leaving one of the Cerberus operatives dead and both Grayson and Liselle knocked out by stun darts, Leng enthusiastically finishes off Liselle with his knife by cutting her throat. They haul Grayson out of his apartment, kill the guards outside the apartment complex, and depart Omega, leaving little evidence behind.

The Experiment
Kahlee soon receives a second message from Grayson marked as urgent. The message has a pre-recording of Grayson saying that if she's listening to this, that he must have been captured by Cerberus. Grayson had sent her this message, along with wiping his computer terminal clean of data, in the few seconds he had before Cerberus knocked him out and dragged him off. The message contains an attachment, which had all of the information Grayson had on Cerberus. Not knowing who she can trust with this data, or if her life was in danger from Cerberus, she turns to David Anderson for help. They put together a meeting on the Citadel, both making sure they weren't followed. They decide they cannot go to the Alliance for help due to undercover Cerberus agents being among the Alliance's ranks. The only viable option they come up with is to ask the turians for help, since Anderson had gotten to know Ambassador Orinia through his recent political negotiations.

When Grayson wakes up, he is strapped hopelessly to an operating chair, with even his mouth bolted down to prevent him from speaking. The Illusive Man is standing near him, and explains what he is about to endure. He reveals that the Reaper technology involves self-replicating nanites and particle entanglement. The nanites would multiply exponentially, quickly taking over his nervous system and eventually spread throughout his entire body. The Illusive Man gave the signal to start, and Grayson's body goes completely limp from electrocution, a way to reduce any attempt from Grayson to move. Cerberus injects tubes directly into his skull and release the nanites, prompting the Illusive Man to say that Grayson should no longer be considered human. Grayson wakes up some time later in what resembles a jail cell, only to quickly feel hungry and thirsty from what could have been days of sleep. He rapidly drinks the water that had been placed in his cell, and then promptly ate the food that was also supplied to him. During the course of time, Grayson started to experience the beginning phases of the indoctrination, starting with subtle whispers he couldn't understand. The Illusive Man is standing in a room above his cell, watching him through a one-way window. He comments to the scientists that Grayson must be resisting the Reapers' influence and that they needed to sap his willpower. Leng brings up that he had recovered red sand from Grayson's apartment, and that he could inject him with it so the Reapers could control him more easily. The Illusive Man agrees, and sends Leng to carry out his proposal. Leng opens the jail cell door, quickly overpowers Grayson, and injects him with liquid red sand, a more concentrated dosage than dust form. Sometime after this a red sand dispenser was placed into Grayson himself as a means to continually regulate amounts of the drug inside him. When Grayson awakens, the Reapers start controlling his body for him, leaving Grayson hardly able to move his own leg. The Illusive Man inspects the progress and tells his staff to put Grayson down in 3 days, as he may become too dangerous afterwards.

Rather ironically, not long after this, the turian squad sent to take out the space station arrived. They, along with several other teams, were sent to take out all the listed facilities that Grayson had sent Kahlee in his final message. Anderson and Kahlee had convinced the turians to help them take out Cerberus, since neither party liked having them around. The three turian frigates docked with the station, allowing the infiltration teams to enter. The Illusive Man awoke to the alarms and put on his combat suit, cursing how he had not been engaged in active combat for around thirty years. He, along with two of his guards, tried to terminate Grayson, but ran into six turian soldiers in the hallway. They managed to kill one of the turians, but a grenade exploded near their position killing the two guards. Alone, the Illusive Man was determined not to be taken alive and braced for combat, only to realize the other five turians lay dead. They had been surprised by Leng from behind and swiftly killed at point blank range by his superior combat capabilities. The Illusive Man and Leng abandoned the station, with the Illusive Man on edge over letting the Reaper controlled Grayson live.

As soon as the turians secured the station, they began looking for prisoners, as requested by Kahlee. They only found one. The Reapers, using Grayson as a puppet, persuaded the turians that he had been experimented on with red sand and that they should help him. They agreed, and brought him aboard their shuttle. As per their reputation, the Reapers attacked and killed all the turians aboard the shuttle. Although the Reapers had enhanced Grayson's body to better suit their purposes, he still sustained damage from the attack. Grayson felt like a prisoner in his own mind as he watched the Reapers use him to pile all the bodies and eject them into space through the airlock. The Reapers then changed the shuttles destination and forced Grayson to sleep so that they could repair his body's various injuries.

The Hunt
Anderson and Kahlee became worried about not only their safety, since they had hit Cerberus hard, but also for Grayson. The turian shuttle had reported rescuing a prisoner, and sent in the retina scan, revealing that Grayson had indeed been on board. However, that shuttle never reported back. Orinia saw Grayson as a traitor, prompting Kahlee to defend him. Kahlee persuaded her to let her go to the station and find out what happened. Kahlee, along with Anderson and turian escorts, departed to the former Cerberus station. They found various heavily encrypted files detailing their research into Reaper technology and their experiments on Grayson. However, the Illusive Man had not thrown in the towel. He persuaded Aria to help him take out Grayson, which was only possible since Aria believed Grayson betrayed her when he left Omega. Aria swiftly sent her forces to the former Cerberus station. They quickly took about all resistance posed by the turians aboard, and took Kahlee and Anderson alive. The plan was simple, use Kahlee as bait to lure Grayson. After sending a fake distress call from Kahlee, they set up their trap. The Reapers took the bait, much to the dismay of Grayson who did not want to see Kahlee harmed. Soon after arriving, the Reapers began to sort through Grayson's memories of Kahlee for anything useful they could find. They took interest in the Ascension project, seeing potential in the biotic capabilities of the students. After finding Kahlee, the Reapers quickly figured out it was a trap, and amazingly killed many of the would-be assassins. They promptly made Grayson escape Omega after dealing with Aria's reinforcements. The Reapers' avatar had survived the trap, and without delay, had him plot a course to Grissom Academy.

Leng witnessed Grayson's escape and knew that he would need help in order to bring him down. He overheard Kahlee and Anderson, who had both survived the encounter, and offered them a ride off of Omega. He claimed they had mutual goals, yet both of them refused to help Cerberus, and a fight ensued. Leng easily defeated both of them, and offered them a ride a second time, tempting them with a lie that Cerberus could reverse what happened to Grayson. Taking the bait, they both agree and go with him. However, when confronted with the guards at the shuttle bay, Anderson quickly threw Kahlee into one of them, then stole his taser. He used the taser on Leng, then surrendered to the guards. He persuaded the guards to let him take Leng's limp body, stating that Leng was with Cerberus and would be interrogated accordingly. Anderson and Kahlee entered Leng's shuttle and took off. They bound Leng's body to the copilot chair with rope from the shuttle's medkit as a precaution, as they set off to the Citadel. Sanders and Anderson are in a discussion when Anderson states that he noticed Kai Leng has awoken, during their discussions they realize where Grayson is heading, to the Jon Grissom Academy where the Ascension Project is being carried out, they quickly change their course and head straight there.

The End of the Chase
Grayson arrived at Grissom Academy, convincing the docking officials that he was there on invitation from Kahlee. Now docked with the station, the only obstacle left was Grayson's Reaper-altered body, which would have alarmed the guards and prevented him from getting past the airlock. Using a blanket as a cloak, Grayson boarded the station and immediately killed the guards, then made his way towards the lab. Once there, Grayson hacked the terminal and started transmitting Academy data to the Reaper fleet.

Meanwhile, Anderson and Sanders entered the Academy, leaving Kai Leng aboard the ship. The team split up, with Sanders going to find the guards and evacuate all of her students while Anderson headed straight for the labs. Unattended Kai Leng managed to set himself free and followed his captors into Academy. Inside the Academy, he found one of Sanders' students, Nick Donahue, who knew very little about the current situation. With a bit of deceit, Leng managed to secure Nick's biotic help 'to take kidnappers out'.

While wandering through Academy halls, they all faced their common foe in turns, none of them managing to get the upper hand. Reaper-Grayson once again proved hard to kill, as he severely crippled Anderson, tried to indoctrinate Sanders, and critically wounded Nick. It was the combined effort that finally took the avatar down, with Anderson landing a couple of shotgun shots and Leng finishing the job with a pistol.

Nick's severe wounds prevented Anderson from simply taking Kai Leng as a prisoner; Leng refused to apply pressure to Nick's wounds stating that Anderson must choose between imprisoning him and saving Nick. Ever the soldier, Anderson chose the third option and the inevitable shootout between Anderson and Kai Leng was resolved when Anderson decided to help Sanders, but not before immobilizing Leng with a pistol shot to each leg. Although crippled, Leng still managed to escape the Academy and contact the Illusive Man, the Cerberus leader grudgingly accepting the resolution of this catastrophe.

Eventually, everyone in Grissom Academy recovered, including Nick and Anderson. Anderson declared his intent to study Grayson's remains, and asked Sanders to join his research team. Finally, Sanders and Anderson shared a kiss.

Epilogue
The Illusive Man decided that Cerberus may yet profit from Anderson's independent research into Reapers. But he was not about to give up his own research efforts. To secure a deal with Aria he payed her a hefty sum for databanks she recovered from his overrun station, at the same time allowing her to keep her own copies.

For he knew that the Reapers will be coming – the more groups to study them, the better.

Mass Effect: Inquisition
Mass Effect: Inquisition takes place in 2186 on the Citadel. Captain Bailey of Citadel Security Services talks with his child, reassuring him that he will be back on Earth in time for the Salmon Run. After the call, Bailey receives a message from Councilor Udina asking him to come by his office as soon as possible. At Udina's office in the Presidium, Udina informs Bailey that C-Sec has been compromised and is working to undermine the Citadel Council. Udina charges Bailey with personally investigating the involvement of Executor Pallin, who has been spotted at a building in Bailey's precinct.

At the building, Bailey discovers two dead C-Sec officers. One holds a datapad with an image of Pallin's face displayed on it. Pallin appears and demands at gunpoint that Bailey hand over the datapad. Bailey confronts Pallin with Udina's accusations, but Pallin denies them and warns that Udina cannot be trusted. Bailey notes that Udina said the same of Pallin, and that it is Pallin's picture on the datapad the dead officer was holding. When Bailey tells Pallin to give his story to the officers who will arrest him, Pallin becomes enraged and shoots at Bailey, hitting him in the shoulder. Bailey returns fire and wounds Pallin in the chest. Pallin then tackles Bailey, but is fatally shot.

Bailey retrieves the datapad but wonders why Pallin didn't kill him when he had the chance, and why Pallin's actions were so uncharacteristically sloppy. Bailey reports his findings and suspicions to Udina, who dismisses Pallin's behavior as another indication of his guilt, a detail for the investigators to look into. Udina promotes Bailey to Commander, telling him to get some rest and to report his findings to the Council. Bailey gazes over the Presidium, dismayed that his new duties would mean canceling his return to Earth.

Mass Effect: Deception
''This section features material from the first edition of Mass Effect: Deception, which BioWare has acknowledged contains discrepancies with other Mass Effect lore. Once revised editions of the book are released, this section will be updated.''

Cerberus assassin Kai Leng journeys to the ancient city of Thondu on the batarian homeworld of Khar'shan to retrieve an item in an auction of rare goods and artifacts. The item in question is the design for a DNA-specific bio-weapon tailored to target the Illusive Man, the leader of Cerberus, and which could potentially affect thousands of people distantly related to him. Leng snatches the design and makes his escape.

On the Citadel, David Anderson, Kahlee Sanders, and Nick Donahue prepare to speak to the Citadel Council about Paul Grayson's attack on the Grissom Academy. At the Citadel Tower, Anderson and Sanders inform the Council of the Reapers' involvement, but the Councilors are unconvinced and prefer to argue that Grayson was acting on behalf of Cerberus, even after they are shown Grayson's Reaper-mutated corpse. Anderson and Sanders are told to continue their investigation. After the presentation, they find that Nick has disappeared. They go to The Cube, a gym for biotics, to see if he had gone there early, but no luck. A volus attendant at The Cube directs them to Ocosta Lem and Arrius Sallus, a salarian and a turian that Nick had been seen with on earlier visits. Lem and Sallus's address turns out to be fake, and Anderson and Sanders come to conclusion that Nick is missing.

Kai Leng meets with the Illusive Man on an abandoned mining world in the Crescent Nebula. The Illusive Man orders Leng to steal Paul Grayson's body and begin observing Anderson and Sanders; their recent activities on the Citadel have drawn unwelcome attention to Cerberus.

Elsewhere in the galaxy, the batarian slave ship Glory of Khar'shan attacks the quarian ship Idenna, carrying Gillian Grayson and Hendel Mitra, who are part of the ship's security team. When the batarians disable the Idenna's drives and board it, Gillian and Mitra help defend the ship. With Gillian's help, the quarians gain the upper hand and charge onto the Glory of Khar'shan. One of the ship's freed slaves is Hal McCann, a former Cerberus operative who worked on the space station where Paul Grayson had been experimented on with Reaper technology. McCann keeps this fact to himself, but does tell Gillian that her father had been killed and persuades her that information on who killed her father could be found on the Citadel. Deciding to track down her father's killer, Gillian commandeers the Glory of Khar'shan and brings Mitra and McCann with her.

Anderson and Sanders find a message from Nick at their apartment. Nick explains that he left to join a group known as the Biotic Underground that advocates biotic supremacy over all of the galaxy's races. Anderson uses contacts in C-Sec to dig up info on where Nick had gone. Videos show Nick leaving with Ocosta Lem and Arrius Sallus, members of the Biotic Underground.

Mass Effect: Conviction
Days after the events of Arrival, the galaxy is in turmoil over Commander Shepard's actions. While the Citadel Council denounces the Commander and Councilor Udina deflects blame from the Systems Alliance, the Batarian Hegemony calls for retribution for the apparent terrorist acts.

On Omega, Alliance soldier James Vega plays cards in a bar as he watches a newscast about the uproar. Without warning, he rips the screen from the wall, offering to pay the krogan bartender for the damages. The batarians Vega was playing cards with become confrontational and accuse him of being a "Shepard Lover". Vega tries to calm them down, but they charge him. He bashes one batarian over the head with the screen, then rushes the leader of another group, both of them crashing through a window. The rest of the batarians surround Vega and attack.

The fight is interrupted by the arrival of Admiral Anderson and a contingent of soldiers. Anderson informs Vega that he is being brought in for more training. As they board an aircar, Anderson tells Vega that he must get past "the incident on Fehl" and "be the soldier we expect of you". Vega argues, demanding that Anderson throw him in the brig as they approach the Normandy SR-2. Anderson then explains that Vega will actually be guarding the brig, and one special prisoner: Commander Shepard.

Attack on Omega
Following the conclusion of Mass Effect 2, the human-survivalist organization Cerberus began establishing a series of bases beyond the Omega 4 Relay to carry out experiments on the Collectors' technology. Although relations between Cerberus and Aria T'Loak, the Pirate Queen of Omega, were damaged during the events of Mass Effect: Retribution, Aria has continued to permit Cerberus the use of Omega as a supply hub for their operations. Mass Effect: Invasion opens as a group of thugs prepare to raid a Cerberus transport ship that recently landed on the station. Without warning, strange creatures emerge from the ship and attack everyone in sight. The creatures make their way to the Afterlife Club, where Aria's assistant Anto and several mercenaries attempt to fend them off. Just as the creatures overwhelm the mercs and one moves in to kill Anto, Aria arrives. With her help, the mercs drive away the creatures. Aria orders her men to take out the remaining creatures one at a time.

Ships bearing Cerberus identification tags enter the area through another mass relay. At first, fearing more creatures, Aria tells Anto to activate Omega's defenses, but realizes that the new ship is attacking the transports. The ship makes contact with Omega Control and is identified as the Elbrus, commanded by General Oleg Petrovsky on behalf of Cerberus. As the Elbrus continues sweeping up the Cerberus transports, Aria questions how the ship arrived so quickly, confiding in Anto that something felt wrong. Just as she returns to Afterlife to call the Illusive Man, Anto exclaims that the Illusive Man was already calling her.

The Illusive Man shows Aria security footage of the creatures, called Adjutants, escaping captivity within a Cerberus base and escaping on personnel shuttles. He explains that all of Cerberus' research bases have gone silent, which is why he sent the Elbrus to help Aria out. Aria accuses him of tampering with Reaper technology, but he defends the action as necessary to understand the Reapers and reveals that more Adjutants will be on their way once they learn to control Cerberus' better-armed ships. Aria's fight is the Illusive Man's fight, too.

Later, Aria encounters Petrovsky and a Colonel Ashe killing a badly-wounded turian and collecting something from the body. Aria is alarmed, but then notices a salarian corpse transforming into an Adjutants. Aria and Petrovsky take it out; newly-transformed Adjutants are weaker, needing more time to rewrite the genetic code of their bodies. Ashe begins ordering Aria's mercs to finish the cleanup, to "Follow Cerberus' lead - and live!" Aria hits Ashe with a biotic attack, enraged that a Cerberus agent would dare give orders to her men. Ashe retorts that he's only doing his job and humanity's job: saving the galaxy from the aliens. Petrovksy intervenes and says that with more ships on the way to Omega, the Elbrus will do what it can to stave them off, but help from Aria would be appreciated until Cerberus reinforcements arrive.

Aria musters several ships to back up the Elbrus, where she and Petrovsky oversee their makeshift fleet. Petrovsky expresses regret that Colonel Ashe was unavailable to assist him, Aria having locked Ashe up for the duration of the crisis for disrespecting her authority. Aria asks Petrovsky if he plans to make a last stand, like he did against a turian assault while he was a corporal. The general reassures her, explaining that he is student of military history and that the strategies they will use now will be used because their formulators lived. As more ships arrive through a mass relay, Petrovksy vows to lift the siege of Omega.

Back on the space station, a krogan and two turians guard Colonel Ashe and mock him for defying Aria. Ashe tells them that he's right where he needs to be, and without warning attacks the guards and kills them all. Ashe picks up an assault rifle and communication headset and contacts the Illusive Man, revealing that he's ready to start the real battle for Omega.

Betrayals
Aria and General Petrovsky aboard the Elbrus lead Omega's defense forces against the Adjutant ships. At first the battle goes smoothly because the Adjutant ships do not return fire. The Adjutants have yet to master the controls and use the weapons. This doesn't last for long, as one ship manages to fire on Elbrus. Many more quickly follow suit and Elbrus takes considerable damage. Aria points out that losing their ships is an acceptable loss when weighed against the millions of lives aboard Omega. She suggests closing the Omega 4 Relay to prevent any more Adjutants from entering the system. Petrovsky points out the holes in her plan: relays are impenetrable and cannot be disabled, and laying mines around the relay to destroy ships that arrive through it would take far too long. Above all, the Illusive Man would forbid such an action, as Cerberus still has a vested interest in its Reaper research. Aria begins to argue, but the Elbrus takes another hit. Petrovsky realizes that the only place they can retreat to now is the relay, where they can escape to the center of the galaxy and possibly stop the source of the problem. The Adjutants won't follow them because they are intent only on advancing on Omega to transform its population into more Adjutants.

In Omega Control, Anto Korragan learns that Aria's ship has left the system. Knowing that Aria would never abandon Omega, he assumes that she is either dead or an Adjutant, and begins forming plans to take over as Omega's leader. In the shadows, the escaped Colonel Ashe listens in.

The Elbrus arrives at Avernus Station, a Cerberus research base almost overrun by the Adjutants. A handful of surviving Cerberus personnel flee to the station's exterior, hoping the area's intense radiation would deter the attackers, but to no avail. The Elbrus' guns take out the Adjutants just in time, and the ship docks with the station's north spoke, the only wing that hasn't been compromised.

Aria, Petrovsky, and the Cerberus personnel investigate the base and discover a survivor, Gabone, an assistant administrator. Gabone explained that when the scientists had begun studying a live Adjutant specimen, it "whispered" to them. Petrovsky suspects this was a method of indoctrination and prepares to execute Gabone in case he had already been affected, but a group of Adjutants break down the doors into the room. While Aria and the Cerberus operatives are distracted, Gabone transforms into an Adjutant and lunges toward Aria. Petrovsky intervenes and kills it, saying he should never leave his business unfinished. Aria then uses her biotics to obliterate the other Adjutants, but the effort causes her to pass out. Petrovsky orders his men to contact the Illusive Man to inform him that Avernus Station is now secure, but the Illusive Man sends a message to him first.

Back on Omega, Cerberus reinforcements finally arrive and set upon the Adjutant ships. Anto, flanked by guards, heads to Omega Control to find out why he, Omega's soon-to-be new leader, was not informed that Cerberus had arrived. Colonel Ashe appears, shooting Anto's guards and running past him. Anto runs to Omega Control, wondering how Ashe escaped and what he was up to, but when Anto reaches the room he stops, shocked. Everyone in Omega Control is dead.

Aria awakens on the Elbrus, still docked with Avernus Station. Biotic dampeners have been fitted around her hands. Petrovsky explains to her that the strategic situation has changed; Aria will be a "guest" on the Elbrus until further notice. He plays a recording that the Illusive Man had sent earlier. In it, Colonel Ashe speaks to the people of Omega, saying that with the Adjutant crisis over, Cerberus has decided that control of the station is vital to protecting the galaxy from the Reapers. He reveals that to institute an orderly transition of power, he has disabled Omega Control and the station's defenses, and Cerberus has eliminated all of Omega's remaining defenders. Ashe commands everyone to submit to Cerberus immediately or suffer the consequences. Omega belongs to Cerberus now.

Cerberus Strikes
Colonel Ashe leads a squad of Cerberus operatives through Omega to secure landing bays for troop transports. They encounter Blue Suns, Eclipse, and Blood Pack mercenaries battling it out in the streets. Ashe questions a nearby batarian who explains that without Aria to maintain the peace, all of Omega's factions are vying for control of the station. When asked if anyone heard Ashe's announcement, the batarian says that everyone thinks Cerberus is there to clean up the Reaper mess since no one understands why Cerberus would want Omega. Ashe's squad moves on to the landing bays. Ashe notes that the Illusive Man had anticipated only a narrow window for Cerberus to act before Omega's inhabitants organized a resistance, and this gang conflict has given them a little more time. Furthermore, Aria is the only person who could lead such a resistance, and Ashe is confident she won't be coming back.

On the Elbrus, still stationed near Avernus Station, Aria groggily awakens in a restraining device. General Petrovsky, who had been reading a copy of the book "War and Peace", greets her and apologizes for the restraints, saying that they were necessary because Aria kept trying to escape and the design is intended to disorient her. Petrovsky tells her that she has been out long enough for the Adjutants to be mopped up both at Avernus Station and Omega. He explains that center of the galaxy is one of its safest places, and controlling it and protecting humanity necessitates controlling Omega. Aria realizes the Adjutants getting loose wasn't a mistake, that their rampage across Avernus Station and Omega was part of the Illusive Man's plan all along. Their discussion is interrupted and the general is called to the ship's bridge to receive a message from the Illusive Man. Before he goes, Petrovsky orders a mental inhibitor be used on Aria to prevent her from using any biotic powers that don't require her hands.

The Illusive Man informs General Petrovsky that capturing Omega was a contingency plan activated after Aria was distracted by the sudden Adjutant threat. Since the source of the Adjutants has been reclaimed, Petrovsky is needed back on Omega to head Cerberus' operation. Petrovsky expresses regrets at the loss of so many loyal Cerberus members and says there has not yet been word about how the Adjutants escaped. When the Illusive Man asserts that the general has doubts about what happened, Petrovsky denies it. He pointedly remarks, however, that he found Aria's suggestion that the disaster was a sham to allow Cerberus to conquer Omega ridiculous, since the Illusive Man would "never endanger so many of our people just for the sake of a diversion..." The Illusive Man responds, "Time and Patience, Oleg", echoing part of a passage of "War and Peace" that the general had been reading to Aria earlier. He tells Petrovsky to transfer Aria to a research station before reaching the mass relay and ends the transmission.

Petrovsky is then called into a corridor by a Cerberus operative. He finds a freed Aria holding the disarmed operative and standing in front of several other incapacitated operatives lying on the floor. She hits the general with a biotic attack and sends him reeling. While Aria flings two crewmen into the air, he grabs a pistol and takes aim, but she counters with kicks to his torso and head. As she grips him by the neck, she says "That's the end of my patience, Petrovsky - and your time."

Gang fighting continues on Omega. Anto complains to a turian that all he wanted to do was get the gangs to listen to him like they did to Aria, but the cease-fire he called for was ignored. The turian points out that Anto isn't Aria. The batarian reluctantly admits that they do need Aria after all. Colonel Ashe appears with more Cerberus troops who open fire on the battling gangs. Anto and the mercenaries retreat to Afterlife, and Ashe orders a team sent after them. An operative informs Ashe that the Elbrus has returned and General Petrovsky wishes to speak with him. Taking a handset, Ashe tells Petrovsky that he is already securing their first sector in Omega and there was no need for the general to come. Petrovsky reminds Ashe that he is command of Cerberus' forces there and confirms that he will arrive shortly to "storm the fortress - just like Anticlus at Troy."

After he cuts the transmission, Aria praises the general for being so willing to follow others' directions. Petrovsky retorts that he is only cooperating because Aria threatened to space the Elbrus' troop compartment and he doesn't want any more people to die needlessly. Aria points out that he isn't concerned about the deaths of her people on Omega. They argue further as the Elbrus docks with Omega and Aria leads Petrovsky at gunpoint through the boarding ramp. As Aria prepares to kill Petrovsky, the doors open to reveal Colonel Ashe and several Cerberus soldiers waiting. Petrovsky knocks Aria out of the way of incoming fire, giving her the chance to escape. The general scolds Ashe for nearly killing him too and asks if Ashe even understood the reference to Anticlus in his message, which meant that the Elbrus had been compromised and he couldn't talk. Ashe dismisses the accusation. The message was the reason why Ashe had a team ready, he couldn't forget Petrovsky's constant historical speeches and recognized his code. Petrovsky orders Ashe to deploy all Cerberus forces on Omega to hunt down Aria T'Loak and secure the station once and for all.

Anto watches the exchange on a monitor and turns to face a room full of mercenaries. He tells them that Cerberus will take over Omega if they don't stop fighting amongst themselves. A krogan responds that Anto can't run a revolution; the only person the mercenaries would willingly follow is Aria, and Cerberus knows that. At that, Aria makes her presence known and announces a "little job" she wants everyone in on. She says that if Cerberus wants Omega, "they'll have to take it over our dead bodies!"

The Battle for Omega
While attacking a Blue Suns hideout on Omega, General Petrovsky's Cerberus soldiers face stiff resistance from an unpredictable enemy. As Blood Pack varren and Eclipse YMIR Mechs stymie the Cerberus troops, they realize the entire hideout has been mined. The mines explode and the squad is lost. Colonel Ashe calls in another team to sweep the area for traps, but is reprimanded by Petrovsky, who asserts that a true soldier would send in medics to aid the wounded first. Ashe retorts that Petrovsky is at fault for the worsening situation because he brought Aria back to Omega. The station's gangs have united under her and Cerberus has been denied an easy victory. As Ashe suggests that the Illusive Man should replace the General, Blue Suns troops emerge from the ventilation tunnels and attack. Ashe and Petrovsky cut them down. Petrovsky surmises that Aria is headquartered somewhere in the station's endless slums, allowing her forces to strike anywhere. She could hold out against the Cerberus invasion indefinitely, but the General knows that as long as the battle rages, no one profits from Omega. To flush her out of hiding, Petrovsky proposes giving her what she wants: victory.

Deep in Omega's slums, Aria and her mercenary allies notice Cerberus forces pulling back. She pounces on one unlucky trooper and interrogates him. It turns out Cerberus isn't retreating: the Adjutants are loose in Cerberus's bases again and all operatives on Omega have been recalled by General Petrovsky to contain them. Petrovsky has declared Omega an open city under Aria's rule once again. Later, Anto confirms that most Cerberus ships have left aside from a few civilians and support ships. Aria suspects a trap and decides to beat Petrovsky at his own game by capturing him and using him as a bargaining chip to force negotiations with the Illusive Man.

Aria's group spies on Petrovsky, Ashe, and several humans, all adorned with armor from Omega's gangs as per the General's "false-flag" scheme. A group of aliens in heavy robes approach the humans claiming that the plague has broken out again in the Gozu District. Without warning they discard their robes and use concealed weapons to open fire on the Cerberus operatives. In the commotion, Aria makes a run for the Afterlife Club, her main stronghold. Believing Petrovsky's plan to have failed, Ashe notifies a standby team to activate option "Omega-Two". The General balks at the idea of using explosives in an area populated with civilians, but Ashe pulls a gun on him and reveals that explosives aren't part of the plan at all. In the battle-damaged Afterlife Club, Aria orders Anto to contact the Illusive Man. When he doesn't respond, she ascends to her booth and finds an Adjutant killing Anto.

Outside, Ashe explains to Petrovsky that they placed an Adjutant in stasis during the earlier mop-up operation. While Petrovsky focused on his false-flag plan, Ashe's own men moved the stasis pod into Afterlife and Ashe remotely freed the Adjutant. Petrovsky is livid that Ashe would put the entire station in danger with such a dangerous plan, but Ashe considers the potential casualties to be acceptable losses. They begin to fight, but the Adjutant is suddenly hurled through Afterlife's front doors and knocks the two men down. An enraged Aria emerges, roaring at them to leave her station. Ashe raises his gun to shoot her, but the Adjutant strikes him first. Aria spears it with a biotic blast. A transforming Ashe asks Petrovsky what he will do. The General responds that he will do what he is sworn to do: protect his troops. He shoots Ashe point-blank in the head. As Aria advances toward him, Petrovsky warns her that his ruse wasn't the only reason he evacuated Cerberus forces from Omega. A Cerberus fleet waits outside the station with enough firepower to destroy it level by level. If Cerberus can't have Omega, Petrovsky won't allow anyone else to use it against Cerberus. He promises to evacuate Omega's civilians before the barrage, but will only spare Omega if Aria surrenders it. Aria concedes and leaves.

Sometime later, General Petrovsky contacts the Illusive Man to inform him that Omega has been secured for Cerberus. He reports that Aria T'Loak is likely dead, possibly one of the Adjutant corpses found in Afterlife, and Colonel Raymond Ashe is missing and presumed dead as well. When Petrovsky expresses his hope that Cerberus's victory over Omega will ultimately result in the loss of fewer of his soldiers' lives, the Illusive Man pauses briefly before smiling and answering, "Of course". A lieutenant informs Petrovsky that there is no sign of Aria on the station and claims she must have run away like a coward. Petrovsky disagrees, pointing out that he had threatened the one thing Aria had cared about, her station, and she had given it up because she knew that Petrovsky would destroy it. The General didn't approve of some of the methods used to win, but with Aria gone, so is "the threat to the station". As he gazes out a window, he predicts that one day, Aria would return. Meanwhile, Aria looks on Omega one more time from a small transport before turning away and flying off.

Return of the Reapers
Six months have passed since the events of Arrival. Commander Shepard has been relieved of command and detained in a Systems Alliance facility in the city of Vancouver on Earth. Without warning, Alliance deep space outposts beyond Sol begin to go dark. Admiral Steven Hackett, the head of the Alliance military, begins to prepare for an imminent invasion. Admiral David Anderson arrives in Vancouver and escorts Commander Shepard with Lieutenant James Vega to a meeting with an Alliance defense committee. Shepard confirms their worst fears: the Reapers have returned to the galaxy and are on their way to Earth.

At that moment, contact is lost with Luna Base and news reports begin to surface of an unknown alien force landing in Earth's cities. The Reapers have already arrived. A Reaper capital ship then descends through the clouds over Vancouver and blasts the Alliance building, killing the defense committee and Alliance staff. Shepard and Anderson survive and contact Ashley Williams or Kaidan Alenko (whichever survived Virmire), telling them to get to the Normandy. As Shepard and Anderson make their way from building to building to get to the spaceport, Anderson tells Shepard that they have to get to the Citadel and seek help from the Council. They reach a comm set near a crashed gunship and hail the Normandy to evacuate. After holding off an attack from Cannibals, the Normandy bombs the area clear of attackers. As Shepard boards the ship, Anderson informs the Commander that he will stay behind to lead the resistance, and hands over Shepard's dog tags. Shepard protests, but Anderson charges Shepard with getting as much help as possible to save Earth and stop the Reapers.

As the Normandy lifts off, Shepard witnesses a child running to an Alliance evacuation area and boarding a shuttle. As the shuttles lifts off, a Reaper destroyer emerges from behind a cluster of buildings and targets the shuttles, killing those who were aboard including the child. Distraught, Shepard steps away from the open shuttle bay doors of the Normandy, and the ship escapes Earth as more Reapers and the wreckage of Alliance ships rain down upon the planet.

The Crucible
Shortly after escaping Earth, Shepard orders Joker to divert to Mars after receiving a communication from Admiral Steven Hackett, ordering the commander to the Prothean Archives on Mars. Hackett insists that Liara T'Soni has found what may be the only way to defeat the Reapers.

Upon arrival, Shepard, James and either Ash or Kaiden take the shuttle down to the planet, receiving a warning from EDI that the base is not responding. They soon discover the reason why upon witnessing Cerberus soldiers executing surviving Alliance personnal; the group fight their way through the enemy, inferring from the small size of the Cerberus force that they must have had help from the inside. Ashley/Kaiden is also surprised Shepard is unaware of this, given their past association with Cerberus, and Shepard must convince their squadmate they have cut ties with the extremist organisation following their defeat of the Collectors.

After entering the station and arriving in time to witness Liara biotically overpower and execute her pursuers, Liara explains why Hackett sent them to find her; she has found in the Archives blueprints for a Prothean device that might allow them to turn the tide against the Reapers. Unfortunately, Cerberus has learned of it too, and now they must hurry to recover the necessary information before Cerberus can. Sending James back to the shuttle to secure their escape route and prevent Cerberus from doing so, Shepard, Ashley/Kaiden and Liara fight their way through the station to the main Archive, discovering along the way the identity of the traitor in the station: Dr. Eva Coré, supposedly a recently arrived researcher, but in truth a mole who sabotaged the station's defences to allow Cerberus entry.

Reaching the Prothean Beacon at the heart of the Archives, the Illusive Man contacts them by hologram, mocking the Alliance for failing to take advantage of the wealth of information the Protheans left behind and commenting that Shepard is fighting a losing battle. He also explains his new motivation; to find a way to control the Reapers and thus use their power to advance humanity to a new level of evolution and above the other races. Deriding the Illusive Man's plan as madness, Shepard vows to use the information to destroy the Reapers and dismisses the Illusive Man's warning not to interfere in Cerberus's plans. The group then encounter Dr. Coré, who had been trying to upload information on the Prothean device, but her upload is interrupted by the squad and she tries to flee. Although Coré is able to reach a Cerberus shuttle, James disables it with a kamikaze attack before it can escape, having also alerted the Normandy to extract the squad. Coré, revealed to be an android by the explosion, emerges from the wreckage and attacks, critically injuring Ashley/Kaiden before being disabled by Shepard. The Normandy arrives to extract the team just as Reaper forces begin landing on Mars.

Having escaped Mars, Shepard forwards information on the Prothean device to Hackett, orders Liara and EDI to begin extracting intel from the android and orders the Normandy to the Citadel.

Uniting the Galaxy
Upon arrival at the Citadel, Ashley/Kaiden is taken for medical treatment at the nearest hospital and Shepard conveyed to a meeting with the Council. Upon arriving, Shepard is quick to see the Councillors are looking to their own borders, despite Udina's insistence that Earth is bearing the brunt of the attack and needs the most help. The salarian Councillor explains that if the worlds of the other Council races can be secured, then they can divert military forces to Earth, and that a summit is being convened to discuss strategy. The Council is also unimpressed by the Prothean device, insisting it must be flawed as it failed to save the Protheans from extinction at the hands of the Reapers, but Liara explains that a missing component referred to as "the Catalyst" prevented its completion.

Upon departing the meeting, Shepard and Udina are met in his office by the turian Councillor, who explains that Palaven's ruler, Primarch Fedorian, didn't escape the system before the Reapers arrived, and requests that the Normandy extract him from his current location on Palaven's moon Menae, explaining that Fedorian will be a useful ally in accruing support for Earth. Before departing, the Councillor informs Shepard that the Council has agreed to uphold/reinstate their Spectre status, granting them the benefits of the position.

The Normandy enters the system to find Palaven and Menae under heavy attack by the Reapers, with the turian military under immense pressure and taking heavy losses. Upon landing on the moon at a turian base, Shepard learns from the commanding officer that Primarch Fedorian is dead, having been killed an hour before Shepard's arrival and they have no idea who has succeeded him because their communications with Palaven Command have been cut. Fighting through swarms of Husks to the comm tower and repairing it, the turians soon learn that General Adrien Victus, a popular military commander with a reputation for playing loose with strategy, has been named as Palaven's next Primarch; however, he is fighting at a base several miles away, with which radio contact has been lost. At the same time, Shepard receives a message from Joker that EDI and the Normandy are acting strangely; Liara returns to investigate, while Shepard's old squadmate Garrus Vakarian joins them, both to help fight and to lead them to Victus's position.

Fighting their way through Reaper forces, Shepard, James and Garrus arrive at the base and after helping Victus and his soldiers fight off their attackers, relay the news to the General that he is the newest leader of his people. Victus is dubious about his ability to lead, claiming to be no diplomat and unwilling to leave his men, but he reluctantly agrees to accompany Shepard to the summit, but insists that he can't divert troops to Earth until Palaven can be secured, something beyond the turian military's ability to do now. Victus insists that the turians will need reinforcements, namely the krogan to succeed.

Upon returning to the Normandy, Shepard and the crew discover the earlier power fluctuations were caused by EDI implanting herself in Eva's body, a process which has completed successfully and given EDI more options, namely the ability to leave the Normandy and accompany Shepard into combat. Soon after, Shepard receives words from Admiral Hackett that Alliance Research and Development has begun construction of the Prothean device, dubbing it "Project Crucible".

Aiding the Krogan
The decision to involve the krogan in proceedings causes major problems; the asari pull out of the summit altogether, believing turian-krogan relations too fragile for anything to be accomplished. A diplomatic meeting is held between Shepard, Primarch Victus, Dalatrass Linron, the leader of the Salarian Union and the clan chief of the krogan, either Urdnot Wrex or his brother and successor Wreav if Wrex is no longer alive. The dalatrass is openly hostile and insulting to the krogan leader, who is ambivalent to the plight of the turians, insisting that the Reapers are moving on Tuchanka and refuses to provide military assistance unless their own demand is met; that a cure is created for the genophage. The dalatrass flatly refuses to agree to such a demand, arguing that what Shepard and Victus are planning to do in curing the genophage is the same rash mistake the salarians made when they uplifted the krogan to fight against the rachni, while Victus believe the plan impossible because it would take years they don't have to synthesise a cure.

However, Wrex/Wreav reveals intel he has received that following the experiments of a salarian scientist into curing the genophage on infertile krogan females, an STG team rounded up the survivors of the experiments- a group of now fertile females who are also immune to the genophage- and took them offworld. The dalatrass, under pressure, reluctantly reveals that the females are being held at an STG base on Sur'Kesh and acedes to their release, though she insists that curing the genophage will have dire consequences for her people.

Shepard, their squad and the krogan leader arrive on Sur'Kesh to oversee the exchange, meeting up with former team mate Mordin Solus who has been put in charge of caring for the krogan females (and is revealed to be the source who leaked information on their existence to the krogan). However, as a side effect of the cure, the females suffered from weakened immune systems and only one has survived. At the same time, a Cerberus strike force hits the base, seeking to kill the surviving female and stop any hope of a cure for the genophage. Shepard and their squad are forced to fight off Cerberus troopers deploying into the base as Mordin and Wrex/Wreav attempt to extract her.

Upon successfully escaping Sur'Kesh and after Mordin synthesise a cure from her tissue, the Normandy deploys to Tuchanka, (recapturing an ancient gound-to-space cannon from Cerberus and preventing the terrorist organisation from detonating a turian bomb planted to prevent further uprisings after the Krogan Rebellions along the way) where the Reapers have begun attacking in force; the plan is to release the cure from the Shroud, a salarian structure built to repair Tuchanka's atmosphere that was used to spread the genophage virus originally, combining a turian airstrike and a krogan ground attack to draw away a Reaper destroyer guarding the tower. En route, Shepard is contacted by Dalatrass Linron, who insists Shepard cannot go through their plan to cure the genophage and reveals that STG sabotaged the Shroud years ago to prevent it being used for such a plan. The dalatrass offers Shepard a deal; prevent Mordin from repairing the Shroud, thus causing the cure to fail, and in exchange, the salarians will provide military support and technical expertise to help construct the Crucible.

The team arrive on Tuchanka, but the Reapers destroy much of the air and ground forces before much damage can be done. Shepard and the squad improvise a new plan; luring the Thresher Maw Kalros into attacking the Reaper destroyer to buy them time, Mordin and Shepard enter the Shroud and Mordin explains that the cure has to be released from the top of the tower; a task that, with the tower collapsing as they speak, is essentially a suicide mission. Shepard must decide whether to let Mordin sacrifice himself to spread the cure, or convince him not to.

The Citadel Coup
Following their mission on Tuchanka, Shepard is contacted by the salarian Councillor, who requests they come to the Citadel to speak with her. The Councillor explains that it concerns Councillor Udina, who has been moving vast sums of money and the Councillor wishes to discuss where it is going, claiming that Shepard "won't like the news".

Upon arriving at the Citadel, however, the station is worryingly silent. Upon scanning emergency channels, the Normandy receives a transmission from an old companion of Shepard's (either drell assassin Thane Krios, who has retired to the Citadel to enjoy his remaining life, or salarian Major Kirrahe, if either are alive) who explains that the Citadel is under attack; Cerberus has hit the station in overwhelming numbers and C-Sec are struggling to retaliate. The contact explains that Ashley/Kaiden (having recovered from the injuries sustained on Mars and been named a Spectre by Udina since then) has gone to protect the Council, while they are attempting to reach C-Sec Headquarters, since C-Sec cannot launch an effective counterattack while Cerberus holds it. Deploying in the shuttle, Shepard and their squad land in the middle of a pitched battle between C-Sec and Cerberus forces outside the headquarters, helping C-Sec Commander Bailey retake the office. Inside, Bailey uncovers intel that the salarian Councillor was meant to be meeting with the Executor, presumably to have someone important prosecuted. Given the message the Councillor sent to the Normandy, Udina is implicated.

Reasoning that the Councillor is likely holed up in the Executor's office, a fairly defensible position, Shepard's squad fight their way through Cerberus's troops, but when they reach the office and extract the Councillor, they come under attack from Kai Leng, who is under orders from the Illusive Man to assassinate the Council. The salarian Councillor also reveals that Udina is collaborating with Cerberus to stage a coup. If Thane or Kirrahe are not alive, Leng manages to assassinate the Councillor; if one or both are, then they thwart Leng's assassination attempt, but are mortally wounded in the process. Leng retreats to pursue the rest of the Council, with Shepard and company in hot pursuit.

Despite Leng's best efforts to slow down and stop their pursuit, Shepard reaches the Council ahead of him at a shuttle pad, locking the exits to prevent Cerberus troopers attacking and a tense standoff ensues, with Ashley/Kaiden standing in their way. Shepard reveals Udina's treachery to the Council and while he attempts to deny it, the rest of the Council, after all the times they didn't listen to Shepard, begin to believe them. When Udina tries to override the lockdown, Shepard must convince Ashley/Kaiden to get out of the way (either managing to talk them down or being forced to shoot them) and Shepard is ultimately forced to kill Udina. With Udina dead and their plan thwarted, Leng and the remaining Cerberus forces retreat, while C-Sec begins securing the station.

En route back to headquarters, Leng reports his failure to the Illusive Man, who assures his agent that Udina was expendable and he has other plans in motion, though the Illusive Man does admonish Leng for letting Shepard defeat him; Leng angrily promises it won't happen again.

The Quarian Offensive
Following the coup attempt, efforts to speed the pace of the Crucible's construction and drive the Reapers back increase. Admiral Hackett contacts Shepard with news on that front, informing the Commander that while turian and krogan ground forces are making progress against the Reapers on Palaven, they need more support ships and the quarians are willing to talk. Hackett requests Shepard meet with the leaders of the Migrant Fleet but urges caution, as recent intel suggests suspicious activity along the geth border.

Meeting with Admirals Shala'Raan, Han'Gerrel, Daro'Xen and Zaal'Koris at a diplomatic ship in the Far Rim, Shepard learns, much to their chagrin, that the quarians are launching another attack on the geth, with the intention of retaking their homeworld Rannoch from their AI creations. The quarians pushed the geth back to the Perseus Veil when a mysterious signal began broadcasting to all geth forces, drastically improving their combat capabilities.

Shepard conclude that the signal is Reaper tech, which must be destroyed if the quarians are to have any chance of survival. The admirals explain that the signal is being broadcast by a geth dreadnought far beyond their ability to destroy. Shepard proposes that they and a squad board the vessel and disable the signal, throwing the geth into confusion and buying the quarians time to withdraw. The Admirals agree and offer Shepard technical support in the form of their newest member; Shepard's old crewmate Tali'Zorah, promoted to her late father's position based on her knowledge of the geth.

Arriving in the middle of a pitched battle between the geth and quarian fleets, Shepard, Tali and their squad board the dreadnought and make their way through the ship, fighting off geth crew to reach the drive core, where the signal is being broadcast. Inside the drive core is another of Shepard's old crew, the geth platform known as Legion, who has been hardwired into the drive core to amplify the Reaper signal; Legion explains that despite their efforts to turn the geth away from serving the Reapers, the quarian attack drove the geth into an alliance with the Reapers in order to save themselves. At Legion's direction, they shut down the drive core, freeing Legion from its shackles, who in return disables all shields and weapons aboard the dreadnought. At that point, however, Admiral Gerrel deviates for the plan and launches a full attack on the dreadnought, hoping to destroy the crippled geth flagship. Shepard and their squad narrowly escape the vessel in time.

After returning to the Normandy and either accepting or condemning Gerrel's explanation of his actions, Shepard requests information from Legion. To the horror of the Admirals, Legion explains that the dreadnought's destruction has only severed the Reaper signal at long range; a base on Rannoch's surface is still transmitting the signal at short range, and the geth will soon recover from the disruption. After breiefly diverting to rescue Admiral Koris, who had been stranded on the planet surface after sacrificing his ship to destroy a geth planetary defence cannon, and shutting down a geth server controlling fighter craft threatening quarian liveships, Shepard and a squad, accompanied by Legion hit the geth base, intending to expose the transmitter to a bombing run by the Normandy. The plan works, but the Reaper tech broadcasting the signal turns out to actually be a Reaper destroyer that emerges to attack, pursuing Shepard's squad as they flee in a geth shuttle. A chance weapons strike from the Migrant Fleet reveal a weak point in the Reaper's defences; that the firing chamber is vulnerable when priming. Using a handheld laser guidance system and dodging the Reaper's attacks, Shepard directs the Normandy and Migrant Fleet's weapons against the Reaper, eventually severely damaging it.

Following its defeat, the badly damaged Reaper and Shepard exchange barbed words; the Reaper, recognising Shepard from Harbinger's description, asserts that Shepard's opposition to the Reapers is pointless, that they are preserving organic life from chaos and that the cycle must continue if organics are to be saved from destruction. Shepard dismisses the Reaper's warnings and assures it that the races of the galaxy will continue to fight until a way to defeat the Reapers is found. With nothing more to be said, the Reaper 'dies'.

With the Reaper destroyed, the geth fleet is left disabled and vulnerable to the quarians, but Legion requests permission to upload a modified form of the Reaper code to all geth that would grant them true intelligence. Sehpard must choose whether to allow this upgrade or not, and if it is, to convince the quarians to cease fire and make peace with the geth, or to stand aside and let one race be destroyed by the other. Whatever Shepard decides, the conflict between the quarians and geth that has raged for three centuries is brought to an end, and the support of one or both races acquired against the Reapers.

Thessia's Fall
Following the resolution of the quarian-geth conflict, the asari councillor requests that Shepard come speak with her on the Citadel. Though the Crucible's construction nears completion, the absence of the Catalyst makes it still useless against the Reapers. The Councillor reveals to Shepard that there is a highly classified artifact located on Thessia that may help the Commander identify the Catalyst; however, she urges haste, as the Reapers have descended on Thessia in droves, seeking to annihilate the most advanced race in the galaxy.

En route to Thessia, Liara who insists on coming to help her homeworld, explains that the artifact is housed in the Temple of Athame, a deity whose worship is nearly as old as the asari, but has fallen out of practice. Arriving on Thessia to find the asari military fighting a losing battle against Reaper forces, Shepard and the squad fight their way to the temple, where a science team is waiting for them there. They arrive at the temple to find a security field blocking entrance, strangely high security for a temple of a dead religion. When Liara deactivates it, they enter the temple and find the scientists dead, but not at Reaper hands. They search the temple which houses artifacts related to Athame's worship, including ones that look suspiciously Prothean. While Liara explains the temple's history, Shepard comes to a realisation; the artifact the Councillor sent them to find is a Prothean Beacon hidden within the temple. Considering the temple's age, the beacon is likely the reason why the asari are technologically and scientifically ahead of the other races and its high security is in order to prevent anyone discovering the asari were withholding Prothean technology in violation of Council law. The squad search the other artifacts to activate the beacon, and when it does, it reveals a Prothean VI referring to itself as Vendetta. Establishing that it is in a post-Prothean cycle and detecting nearby Reaper forces, it attempts to shut down, but Shepard insists that it wait and provide information on the Catalyst and Crucible.

Vendetta explains that the Crucible is not of Prothean design, but had been created by countless galactic cycles stretching back millenia. The Protheans themselves never used it because their efforts were sabotaged by a splinter faction who (like Cerberus in the present cycle) argued the Protheans should control the Reapers, not destroy them. By the time it was discovered the separatists were indoctrinated, it was too late; the Prothean order of battle was irreparably fractured.

Vendetta also mentions that the Protheans learned that similar patterns of evolution and dissolution occur in every galactic cycle, with each path of advancement and conflict happening differently but in fundamentally similar ways - too similar to be merely chance. Vendetta infers that the Reapers are "servants" of the pattern, not its creator, but cannot identity their true master or motive, only its intention: galactic annihilation. Before Vendetta can specify what the Catalyst is, it detects an indoctrinated presence nearby and shuts down.

The intruder is revealed to be Kai Leng who demands their attention, pulling a drone from his coat and remarking that "Someone would like to talk with you". The drone projects a hologram of the Illusive Man, who has learnt of the Thessia beacon from the Mars Archive and mocks Liara for missing it. The Illusive Man goes on to expand on his belief and convince Shepard that controlling the Reapers is the best course of action and that the Thessia beacon contains the information to do so. Shepard asserts their conviction to destroying the Reapers and dismisses the Illusive Man's scheme, accusing him of being indoctrinated. Rebuffed, the Illusive Man orders Leng to kill Shepard and recover the data; a vicious battle ensues, but Leng is unable to gain the upper hand. Leng calls in assistance, ordering a Cerberus gunship to destroy the temple's structural supports, forcing Shepard and their squad to focus their attention on escaping the temple and allowing Leng to access the beacon. By the time Shepard has regained safety within the collapsing temple, Leng has already acquired the data and fled aboard the gunship. Shepard and their squad can only watch helplessly as Leng's ship escapes and more Reapers descend to complete the destruction of Thessia.

After escaping to the Normandy, the asari Councillor contacts Shepard, though the Commander delays the meeting out of reluctance. The Councillor eagerly requests information on the Catalyst and when it will complete the Crucible, but Shepard is forced to tell her of Cerberus's interference and their failure to acquire the data. Realising that asari civilisation, maybe all civilisation may now be lost, the asari Councillor cuts communication, leaving Shepard to brood sadly on their failure.

Chasing Cerberus
Following the disaster on Thessia, Shepard angrily asserts, backed up by their crew, that Cerberus needs to be destroyed before the terrorist organisation's interference does any more damage to the war effort. The Normandy's communication specialist Samantha Traynor alerted Shepard to the fact she had traced the route taken by Leng's shuttle as it fled Thessia as far as the Iera system, but she had lost it there, because the signal was being actively blocked. Despite the fact the only thing of note in that system was Sanctuary, a refugee camp on the planet Horizon for those fleeing the war, at the insistence of Traynor and EDI that the lead was worth investigating, the Commander agreed to check it out.

Upon arriving at the facility, Shepard and their squad find signs of battle between Cerberus and Reaper forces, a surprising discovery given Cerberus's collaboration with the Reapers. Investigating the facility, Shepard found evidence left by former squadmate Miranda Lawson and her sister that the 'refugee camp' was in truth a Cerberus laboratory run by their father Henry Lawson, working for the Illusive Man. Further evidence uncovered that the refugees were being experimented on and ultimately turned into husks, in order to further Cerberus's research into indoctrination, before revealing a bombshell; a signal being broadcast from a tower within the facility, using Cerberus research, had allowed Cerberus the ability to control the husks created in their horrific experiments. Lawson had been working on the Illusive Man's orders to find a way to transfer this process to the Reapers themselves before the facility had come under attack, the Reapers seeking to destroy any potential weakness that could be used against them.

Fighting their way through Cerberus troopers who hadn't evacuated in time and Reaper forces left behind after the attack, Shepard and their squad fought their way to the tower broadcasting the signal, as well as blocking all transmissions from the planet, finding Henry Lawson holding one of his daughters hostage and the other injured nearby. Lawson explained that despite his success, the Illusive Man had merely ordered Kai Leng to retrieve the data (the assassin having already been and gone) and leave the Lawsons to their fate, and tried to cut a deal with the Commander for his freedom. After executing Lawson for his part in the horrific war crimes committed, Shepard, with the help of Miranda, managed to use a tracer placed on Leng before his departure, as well as shipping information from Sanctuary, to ascertain the location of Cronos Station, the headquarters of Cerberus itself.

Alerting Admiral Hackett to this discovery, the Alliance began making preparations for an all-out assault on the station to eliminate Cerberus, and to recover the Prothean VI and any other information on the Catalyst. However, Hackett warns that once an assault on Cerberus is launched, the Reapers would take notice sooner or later; for all intents and purposes, the attack on Cerberus would be the first step in the campaign to retake Earth. Once military preparations were complete to Shepard's satisfaction, the assault begins.

Leading an armada to assault the facility, Shepard accompanied by EDI and another squadmate, infiltrated the station and fought their way through the labs and power core of the station, uncovering intel on EDI's past, Project Lazarus and Cerberus's new-found obsession with exploiting Reaper tech and indoctrination, as well as pieces of the Human-Reaper salvaged from the Collector Base after its destruction, the team reaches the Illusive Man's personal office, where the Prothean VI is likely being stored. The Illusive Man contacts Shepard again by hologram, sneering that he had already acquired the Catalyst and all he needed to control the Reapers, and despite Shepard's assertion, the idea behind Cerberus would survive even if the organisation itself didn't.

After the Illusive Man severs communication, the Commander's efforts to search through Cerberus databases for the Prothean VI is interrupted by Kai Leng, seeking to kill Shepard. Despite a close-fought battle, Leng is this time unable to get the upper hand and is left critically injured. When Shepard turns their back on the assassin to resume the search for data, Leng silently gets back to his feet and tries to kill Shepard from behind; in the nick of time, Shepard senses the attack coming and dodges, knocking aside Leng's sword and spearing the assassin through the chest with an omni-blade.

With the threat dealt with, Shepard and EDI are able to retrieve Vendetta, who explains to their shock that the Citadel is the Catalyst. When Shepard points out that the Reapers created the Citadel, Vendetta hypothesizes that at some point in a previous cycle, the Crucible was deemed to not be powerful enough, so the Citadel was incorporated into the design, using the Reapers' own technology against them. Unfortunately, it is too late; the indoctrinated Illusive Man has already alerted the Reapers, and they have moved the Citadel to the occupied Sol system to better protect it.

The Battle for Earth
Shepard alerts Hackett and Anderson to their discovery of the Catalyst's identity and location. With no alternative, Hackett and Shepard order the forces they have gathered to the Sol system with the intention of taking Earth back from the Reapers. Hackett and Anderson brief Shepard on the three-fold plan of battle; 'Sword' Fleet will engage the Reapers in space, while 'Hammer' ground forces will land in London. When Shepard queries why London is their landing zone, Anderson explains that the Reapers have established a teleportation beam between the city and the Citadel to transport dead and living humans to the station, presumably to be harvested. The plan is for Hammer ground forces to fight their way through the city to the beam, and get as many people as possible on board the Citadel and find a way to open the station's arms. Once this is done, Hackett will signal 'Shield' Fleet, which will remain outside the Sol system protecting the Crucible, to deploy and clear a path for the Crucible to dock with the Citadel.

All forces deploy for the Sol System and a brutal space battle ensures between the fleets Shepard has gathered and the Reapers in orbit around Earth. The Normandy breaks off from the battle and descends to Earth, Shepard and several other squads having been ordered to take out Reaper Destroyers planet-side, fitted with anti-aircraft Hades Cannons that threaten Hammer's landing. After eliminating the destroyers, Shepard and their squad are extracted by Anderson and local resistance forces, who convey them back to their forward base. At the same time, Hammer troops begin landing en masse in preparation for the assault on the Citadel beam.

Once as much of Hammer has survived have deployed, Anderson briefs Shepard and the other commanders that they must fight their way through the city to the beam, though they will need to take out another Reaper Destroyer blocking their path en route. Using Thanix missile batteries and EDI'S guidance to overcome interference in the guidance systems from the Citadel, the Reaper is brought down, but by that time, Hammer's forces have suffered heavy casualties, Reaper reinforcements are en route and to make matters worse, Hackett warns that several Sovereign-class Reapers, including Harbinger, have broken away from the space battle and are descending to Earth. By the time the remnants of Hammer reach the Citadel beam's immediate vicinity, Harbinger has already deployed to protect it.

Hammer attacks, but Harbinger annihilates them; countless soldiers are killed and Shepard is critically injured. With its stealth technology activated, the Normandy moves in and carries Shepard's injured squad to safety. Believing itself victorious, Harbinger retreats back to the space battle, not noticing Shepard managing to get back to their feet and stagger into the beam, along with Anderson. Upon arriving aboard the Citadel, Shepard and Anderson find themselves separated, dumped in what look like waste tunnels; keepers prowl about and there are human corpses dumped everywhere. Staggering to what looks like a control room, Shepard and Anderson are ambushed by the Illusive Man, the skin of his face and neck rotted and riddled with Reaper tech, who takes control of their motor functions, even forcing Shepard to shoot Anderson. The Illusive Man again asserts the necessity of controlling the Reapers and that the Crucible will grant him that power, but it is clear to Shepard and Anderson that he is deeply indoctrinated. Shepard can try to convince the Illusive Man, like Saren before him to fight his indoctrination, prompting the Illusive Man to commit suicide to escape the Reapers' control, or fighting off his hold, Shepard shoots the Illusive Man.

With the Illusive Man dealt with, Shepard opens the arms of the Citadel and Hackett orders Shield Fleet, along with the Crucible to move in. The Crucible successfully docks with the Citadel, but nothing happens. By this point, Anderson has died of his injuries and Shepard has passed out from blood loss. However, while unconscious, Shepard is transported to another part of the Citadel; when they regain consciousness, Shepard is confronted by an entity of energy, manifesting itself in the form of the small boy Shepard saw die at the Reapers' hands when they fled Earth. The entity explains that it is the Catalyst, the creator of the Reapers and architect of their galactic purges every 50,000 years. The Catalyst explains that the purpose of such genocide is to solve the problem it was created to stop; the creation of synthetic life by organics and the inevitable conflict that would ensue from such.

To prevent this, advanced organic species would be harvested at the apex of their civilisation, with millions of bodies and minds from each race being processed and converted into new Reapers, even as the Reapers themselves worked to destroy their civilizations. By doing this, the Reapers preserved the harvested races, while allowing more primitive races to advance and ensuring that the threat of complete annihilation of organics by synthetics was averted.

However, because the races of the present cycle have completed the Crucible, a feat never before achieved, the Catalyst no longer believes the cycle will work, and thus a new solution must be devised. The Catalyst offers Shepard three choices, leaving the Commander to decide the fate of the galaxy:

1. The Catalyst states that Shepard can use the Crucible to destroy the Reapers. However, it adds that all synthetic life (such as the geth and even Shepard, who is partly synthetic) will also perish, and that the cycle of conflict between organic and synthetic life will begin again, but with no way of stopping it.

2. Alternately, the Catalyst adds that Shepard can use the Crucible to control the Reapers; though the process will kill them, their consciousness will be able to command the Reapers as they wish. When Shepard remarks that the Illusive Man was right after all, the Catalyst comments that it would never have worked for him, as the Reapers were already controlling him.

3. Finally, the Catalyst explains that Shepard can create a union between organic and synthetic life; by merging themselves with the Crucible's energy, Shepard will create a new organic-synthetic "DNA" for all denizens of the galaxy, bringing an end to the cycle and the need for the Reapers.

4. Shepard also has a fourth option not presented by the Catalyst. Rather than choose from the Catalyst's options, Shepard rejects them and insists that a decision with such massive ramifications for the galaxy and its inhabitants cannot be made. The Catalyst acknowledges this, and the Crucible is not activated. The Reapers defeat the fleet that the galaxy's races amassed against them, and succeed in their harvest.

If Shepard chooses to destroy the Reapers, the Crucible fires a red beam of energy that destroys the Reapers on and around Earth and transmits to the mass relay network through the Charon Relay before damaging the relays and the Citadel as well. If Shepard chooses to control the Reapers, the Crucible releases a blue wave of energy that brings the Reapers under Shepard's control, damages the relays, and leaves the Citadel intact. If Shepard chooses to merge organic and synthetic life, the Crucible fires a green beam of energy that causes the Reapers cease attacking, but also damages the Citadel as it transmits the beam to the mass relay network.

While Shepard chooses how to activate the Crucible, Admiral Hackett notices the Crucible activate and orders the fleet to disengage and rendezvous outside of the blast zone. Joker hesitates until the last possible second, desperate to save Shepard, and reluctantly follows the fleet. The Normandy, trying to flee the blast through a mass relay jump, is caught by the energy released from the Crucible and crash-lands in a jungle on an unidentified world.

Epilogue

 * If Shepard uses the Crucible to destroy the Reapers...

Admiral Hackett relates how the Reapers were defeated. Even though the galaxy is devastated and the mass relays are severely damaged, Hackett is confident they can rebuild, but regrets that so many people will not be able to witness the future that Shepard made possible. Eventually, the mass relays and even the Citadel are restored, and the galaxy enters a new era of peace.

If the player's Effective Military Strength is high enough, Shepard is shown to have survived the Crucible's blast, taking a deep breath in a pile of rubble.


 * If Shepard uses the Crucible to control the Reapers...

Shepard, now a Catalyst-like being with absolute control over the Reapers, achieves a new state of existence and ponders immortality. Shepard commands the Reapers to rebuild and protect the galaxy, either intending to give its people hope for the future or acting as the strong leader that Shepard believes the galaxy needs. The Reapers restore the mass relay and the Citadel, and under Shepard's direction, stand ready to defend against anyone that threatens the new peace.


 * If Shepard uses the Crucible to merge organic and synthetic life...

EDI speaks of how Shepard's sacrifice changed the relationship between organics and synthetics forever. Now that both forms of life understand each other, the Reapers have stopped attacking the galaxy and begin to help rebuild of their own accord, and have also begun to share the collective knowledge of countless previous cultures. EDI speculates that with the differences between organics and synthetics disappearing, mortality itself could one day be transcended to a new level of existence she cannot imagine.


 * In all three cases...

With the war against the Reapers over, the people who helped Commander Shepard succeed take on the task of rebuilding a shattered galaxy and adapting to the new peace.
 * Major Coats, Gabriella Daniels, and Kenneth Donnelly will be seen helping in the reconstruction.
 * Zaeed Massani lounges on a chair.
 * If saved, the quarians have begun to rebuild their world (Destroy and Control options). If peace with the geth was achieved, the quarians can be seen without masks, side-by-side with the them (Synthesis).
 * Urdnot Wrex and Grunt are welcomed back home on Tuchanka.
 * The krogan have begun their work on rebuilding Tuchanka.
 * If the Genophage was cured and Eve survived, she can be seen holding a krogan child.
 * Jacob Taylor can be seen working as an instructor (Destroy and Control), or working with Brynn Cole (Synthesis).
 * Jack is seen in a graveyard, laying flowers at tombstones (if her students were sent to the front lines), or working with Kahlee Sanders and her students (if her students were kept in a support role and Kahlee survived).
 * Miranda Lawson can be seen working with Oriana, or planning constructions with other technicians.
 * If she was prevented from committing suicide, and her daughter was saved, Samara can be seen visiting the new Ardat-Yakshi monastery.
 * Kasumi Goto can be seen reuniting with Keiji Okuda (Synthesis, and if the Greybox was saved), or still holding the Greybox in a room (Control and Destroy).
 * Mordin Solus, Thane Krios, Legion, and any other squadmate that wasn't saved in the course of Mass Effect 2 and Mass Effect 3 will be seen in individual shots, seemingly nodding their approval at Shepard's actions.

Meanwhile, the Normandy's crew gather in front of the memorial wall to mourn one last person who sacrificed their life in the struggle against the Reapers: Commander Shepard. Shepard's name plaque is placed on the wall above one for Admiral Anderson. If the Destroy ending is chosen, Shepard's love interest refuses to place Shepard's name on the wall and smiles. Afterwards, they finish repairing the Normandy and take off from the unknown planet.

Many years into the feature, an old man known as the Stargazer tells the story of "The Shepard" to a young boy.


 * If Shepard refuses to activate the Crucible...

One of Liara's time capsules activates an an unknown world. A recording of Liara explains that the capsule contains a record of her generation's war against the Reapers and ultimate defeat. She urges whoever can find the capsule to use the information she gathered on the Reapers and the blueprints of the Crucible to try and succeed where the people of her time did not.