Storyline II

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Mass Effect 2 (Prologue)
The story of Mass Effect 2 begins in 2183, not long after the events of Mass Effect take place. While on patrol to locate and destroy any remaining geth, a race of AI, the Normandy comes under attack by an unknown assailant. The ship suffers extensive damage, forcing the crew to evacuate via escape pods. Joker, the helmsman, continues to pilot the ship despite the received damage to it and is rescued by Commander Shepard, who drags Joker out of his seat and into an escape pod. Before the Commander may board the escape pod, however, Shepard is sent flying amidst a series of explosions and debris slicing through Shepard's suit as the Normandy is attacked once again. Shepard suffocates and dies; the Commander's body is seen entering the atmosphere of a nearby planet.

Commander Shepard's body is located and retrieved by Cerberus, an extremist pro-human organization, and, over the course of two years, attempts are taken to bring Shepard back to life through a project known as "Lazarus."

The Ascension Project
The various Council races are left stunned at the attack on the Citadel -- which is officially described as an attack by a rogue Spectre leading an army of geth, with no mention of Sovereign or the Reapers. As the Council is restructured, and the final pockets of geth resistance found and destroyed, the Alliance Navy has now become a dominant military force in the galaxy and humanity's place in Citadel space is undeniable.

Spurred on by these events, the Illusive Man, leader of a rogue group called Cerberus, decides to push ahead with his plans for Gillian Grayson, a biotic prodigy undergoing training at the Ascension Project. Her father, Paul Grayson, is given a vial of medicine to administer to his daughter, supposedly to improve her biotic abilities and speed the development of 'humanity's saviour'. Kahlee Sanders, now a supervisor on the Ascension Project, is becoming concerned about Gillian's development and her place with the other students. Though gifted, Gillian also suffers from autism that makes her training difficult.

Meanwhile, Paul Grayson's one-time partner and fellow Cerberus operative, Pel, goes to Omega in the Terminus Systems to meet a contact, a quarian named Golo. Exiled from the Migrant Fleet for trying to sell his fellow quarians to the Collectors, Golo is quite prepared to grant the Illusive Man's request for transmission and access codes to the Flotilla. Though he cannot provide the codes himself, he suggests a strategy: lure a scout ship from the Migrant Fleet and ambush the crew.

Troubled by Cerberus' plans for his beloved daughter, and his growing addiction to red sand, Paul Grayson travels to the Grissom Academy and is met by Kahlee Sanders, her lover Dr. Jiro Toshiwa, and the Project's security chief, a former BAaT attendee named Hendel Mitra. Hendel makes no secret of his dislike of both Toshiwa and Grayson to Kahlee; he is well aware of Grayson's drug addiction, and warns Kahlee that there is something about Toshiwa that he doesn't trust. During his visit to Gillian, Paul Grayson secretly passes on the vial of medicine to Toshiwa - another Cerberus colleague - but still has misgivings about giving it to Gillian.

Two Traitors
The quarian Feda'Gazu vas Idenna arrives on the planet Shelba with her ship Cyniad (a scout vessel of the Idenna) after being offered a trade for essential technology by the traitor Golo. Though prepared for treachery, she and her crew are not prepared for an ambush by Pel and his men, and once dead are stripped of their suits for disguises. Pel and his team then approach the Cyniad in the quarian rover, and capture the pilot, Hilo'Jaa vas Idenna. However, when Hilo screams abuse at Golo, the traitor hits Hilo in the face, cracking his faceplate and allowing contaminated air inside.

Back at the Ascension Project, Gillian Grayson is eating lunch when she is confronted by another student and fellow biotic, Nick. When Nick teases her and biotically knocks her milk over, Gillian retaliates with a full biotic storm, culminating in a high-level singularity until she is finally stunned by Hendel Mitra and hospitalised. After spending the night with Jiro, Kahlee goes to see Hendel, who is despondent over his ’failure' in the cafeteria. During their talk, Kahlee suddenly realises that Jiro mentioned her relationship to Jon Grissom - something known only in classified Alliance documents - and discovers both Jiro and Gillian have disappeared from the hospital. Hendel catches up with them in the atrium, where Gillian - having just received a cerebrospinal dose of the Cerberus medicine from Jiro - is suffering a seizure. Jiro stuns Hendel, but is caught by Kahlee, while Hendel saves Gillian's life with CPR. With Jiro in custody and undergoing interrogation, the Illusive Man orders Paul Grayson to play the distraught parent and remove Gillian for more focused observation and testing in a Cerberus facility.

Meanwhile, Pel is approached by Golo, much to the human's disgust. Pel tells him that the interrogation of Hilo is not going well: thanks to Golo, the pilot has caught some sort of disease and is incoherent with fever. Golo apologizes, and explains that he has come to Pel with a tempting offer that doesn't involve Cerberus... an offer direct from the Collectors.

Paul Grayson arrives at the Ascension Project and, hearing that Jiro has confessed to working for Cerberus, demands Gillian be released to him for her own safety. Hendel gets angry, but Kahlee suggests a compromise: Grayson can remove Gillian and take her to safety from Cerberus in the Terminus Systems - if Kahlee and Hendel go along. Grayson reluctantly agrees.

Elsewhere, on Omega, a young quarian on his Pilgrimage named Lemm'Shal nar Tesleya finds Golo, and confronts him about the Cyniad attack. Golo claims he was only the middleman, and tells him about Hilo, still being held captive by Pel. Lemm decides to mount a rescue mission. Grayson, along with Kahlee, Hendel and his daughter, arrives at Omega to meet Pel, pretending Pel is just his contact there. But when they meet Pel, Grayson is double-crossed. Pel is no longer working for Cerberus: he is going to sell Hendel, Kahlee and Gillian to the Collectors. All four are imprisoned, only to be freed when Lemm storms the warehouse, believing he has found four quarian captives. To Kahlee's surprise, Lemm appears to recognise her, and orchestrates an escape. Grayson is left behind; he takes his revenge on Pel by shooting him. After a search Grayson finds Hilo in a cell, horrifically tortured and sick, but still alive and muttering both a frequency and a code phrase.

Travelling with Lemm and the others, Kahlee wonders where they could possibly escape an organisation as powerful as Cerberus. Lemm offers a suggestion - the Migrant Fleet.

Quarantine
Lemm recognises Kahlee because the quarians have an interest in Saren Arterius and his ability to control the geth. He believes that Kahlee could offer some useful insight into how Saren controlled them - and introducing Kahlee to the captain of the Idenna will hopefully be a sufficient Pilgrimage gift. However, once they reach the Migrant Fleet, their shuttle is locked down for quarantine and Hendel, Kahlee and Gillian are asked to stay aboard, not knowing that Paul Grayson has reported to the Illusive Man and asked for help to retrieve his daughter from the Migrant Fleet, using the codes Hilo was muttering. The Illusive Man is eventually convinced to let him go as part of the extraction team, along with Golo.

Hendel passes the time in quarantine by giving Gillian specialised biotic tuition, until Kahlee is summoned to a meeting with members of the Conclave and Admiralty Board. They ask her about Saren, the Reapers and the geth, but Kahlee cannot tell them anything useful. After the meeting, Kahlee, Hendel and Gillian are invited to a private meeting with Ysin'Mal vas Idenna, the Idenna's captain. He explains that the three have inadvertently stepped into a debate raging about the future of the Migrant Fleet. Within ninety years, the quarians will outgrow their ability to sustain themselves, and a solution is desperately needed. Some quarians, including Captain Mal, believe the future of the Fleet relies on ships leaving the Flotilla to search for new homeworlds, whereas the Conclave and the Admiralty Board want to focus on keeping the Migrant Fleet insular and strong.

Their conversation is interrupted when Golo and several Cerberus commandos storm the Idenna aboard the Cyniad. Kahlee and Hendel join the quarians in their battle, sending Gillian to safety, but the girl decides to return to the shuttle where she felt safe, killing several Cerberus commandos on the way with her biotic abilities. Paul Grayson sees his daughter aboard the shuttle as he prepares to steal it, and stuns her, in the hope he can get her to safety. With the battle going badly, Kahlee goes looking for Gillian, only to be ambushed by Golo. As the quarian kicks her, she appeals to Grayson to see the truth: his loyalties to Cerberus are misplaced, they are not turning Gillian into a saviour, but into a weapon. Grayson wavers, then finally turns on Golo and shoots him in the head. Grayson reveals that the Cyniad is wired with explosives, intended to rip a hole in the Idenna and cripple her. Hendel and Captain Mal race to the Cyniad and manage to disable them in time.

Parting Ways
The quarians are then left to deal with the aftermath, and the stunning fact of an attack on the Migrant Fleet itself. Realising the time for conservatism is over, the quarians decide to follow the proposals of people like Mal, and send ships off to search for new homeworlds - or a way to drive out the geth using a Reaper. The Idenna is selected as one of the first to leave, with a hand-picked crew. Hendel and Gillian are selected to go along: Gillian has responded well to the quarian life aboard the Idenna, and after five years to grow up, she might be better equipped to deal with Cerberus.

Meanwhile, Kahlee has been given custody of Paul Grayson. She and Lemm - also selected to go on the Idenna's mission - will take Grayson to the Alliance colony of Cuervo and hand him over to the authorities. However, knowing that Cerberus will get to him eventually, Grayson manages to overpower both Kahlee and Lemm, leaving them to wake up unharmed on the volus world of Daleon. Kahlee asks Lemm to return her to the Ascension Project. There are still children who need her help.

Waiting for a report on the Idenna attack, the Illusive Man is surprised to get a call from Paul Grayson. He has a simple message: he is leaving Cerberus, Gillian is beyond their reach, and if anything happens to Kahlee Sanders, he will go to the Alliance with all he knows. The Illusive Man reluctantly agrees not to pursue either Kahlee or Gillian. He knows that losing Gillian will set their biotic research back a decade, but he cannot risk exposure:

Cerberus has many other projects to protect...

Peace Talks
Galactic tensions are rising due to batarian Ambassador Jath'Amon's arranging of a meeting with the Citadel Council, with the intention of negotiating peace terms between the batarians and the Alliance.

Jacob Taylor is on vacation aboard the passenger liner Arcturian Jade when the ship is attacked by batarian terrorists. Jacob grabs his assault rifle, kept from his former job as an alliance marine, and battles the batarians while defending the crew and passengers. After taking out the batarian attackers, Jacob is thanked by the Captain, Reginald Tudge, who gives Jacob the choice of any quarters on the ship in gratitude.

Jacob arrives at the Citadel and is greeted by his former CO, Major Derek Izunami, who is seeking Jacob out for a mission in the Nemean Abyss, as Jacob is no longer restricted by Alliance military boundaries. He asks Jacob to meet Miranda Lawson, an informant who may have information on the batarian's recent crime wave, in a bar called the Fringe on Cartagena Station.

When Jacob arrives, the Fringe has been taken over by a band of pirates led by Clint "Black Eye" Darragh. Jacob can either convince him to retire or take him on in combat. Once he is taken away, Jacob is greeted by Miranda, who was watching the confrontation from the bar.

Miranda explains the batarian extremists' plan to attack the Citadel on the day of Jath'Amon's arrival and sabotage the peace talks by killing him. She gives him three sources on where to start the investigation: A turian arms dealer named Illo Nazario on the planet Tortuga who has worked with the batarians for years, the planet Bekke where a batarian army is reportedly gathering, and a rumor that the batarians have kidnapped several scientists and are holding them on the Ahn'Kedar Orbital Platform.

Tortuga
On Tortuga, Jacob is met by a salarian friend of Miranda's, Ish, who has the access codes for Nazario's compound. Apparently, Nazario hasn't made any deals for weeks, which has drawn suspicion. As Jacob makes his way through the compound full of turian guards, a unit of batarians will attack. Their leader claims they came to talk to Nazario. Jacob can convince them to turn back or fight them.

Jacob reaches Nazario, who is deathly ill. Nazario reveals that the batarians have tested a weaponized virus on him and bargains with Jacob for a vaccine: Jacob will have Nazario's information about the virus, as soon as Jacob gets him the cure.

Ahn'Kedar
When Jacob arrives at the Ahn'Kedar Orbital Platform he immediately suspects the research carried out there is just a front. A batarian businessman challenges him, but before he can act, a krogan named Nax appears and begins gunning down the batarians. Nax gives Jacob till the count of five to "justify his life". When he either reaches two or is convinced by Jacob, they realize they have a similar goal; Jacob is there to rescue the scientists, among whom is Batha, an asari and old friend of Nax who he infiltrated the facility in order to rescue.

After defeating several waves of batarians, including their leader, Jacob discovers the scientist Dr. Hendricks, who seems more upset about Jacob interrupting their work than having been taken hostage. Hendricks claims the batarians have fallen prey to a terrible disease, which has wiped out entire populations. The disease, a blood plague, is communicable only in high concentrations, incubates very quickly, and has a 100% fatality rate. He claims the batarians brought the scientists there to develop a cure.

Once Jacob convinces Hendricks to leave, he discovers the prototype formula for the cure is held by Batha, who is in another facility. At that moment Nax bursts through the door with Batha in his arms, under heavy fire from the batarians. Jacob saves him and brings him on board his ship.

Once on board, Batha reveals the batarian claim of a virus was fake. The batarians only wanted to convince the scientists to make a cure for their blood plague weapon. The crew realizes they need to get the cure to the Citadel in anticipation of the attack. Though the cure is only a prototype, Batha nearly finishes it using supplies from the ship's med labs, but she requires a final ingredient - a large quantity of unrefined element zero.

Bekke
When Jacob's crew arrives on the rainy mining colony of Bekke, the ship immediately comes under gunfire as Miranda picks up strange readings from the planet. Jacob fights his way into the facility, but begins feeling sick and dizzy due to the batarians' stash, a huge cache of improperly stored element zero. The closer Jacob gets to the eezo, the more strain it puts him under due to his biotic abilities, though it has the beneficial effect of strengthening his powers. Once Jacob defeats the resident batarians, Miranda urges him to leave the facility at once so she can pick up the shipment of element zero. Batha then uses the haul to complete the cure.

The Mastermind Revealed
Returning to Nazario, Jacob can finally interrogate him. Jacob discovers from him that the batarians' true target is the Citadel Council, and not Ambassador Jath'Amon as previously thought. Knowing Jacob holds his only hope of survival, Nazario also reveals that the leader of the batarian extremists is in fact Jath'Amon himself, who intends to infect the Council with the bioweapon during his peace talk. Jacob and Miranda hurry back to the Citadel to stop the meeting.

Defending the Citadel
Jacob heads to the Citadel Tower, but all seems quiet. Jacob is stopped by a C-Sec officer, who is exposed as a batarian, revealing they have infiltrated Citadel Security itself. Battling his way up to the tower, Jacob enters the council chambers in the middle of the ambassador's speech and the asari council representative questions Jacob's intrusion. Jacob brings the evidence against Jath'Amon to light, and Jath'Amon's peaceful demeanor fades as Jacob lays out his plan. The asari council representative apologizes, but says she won't risk the Council until she is sure of Jacob's claims.

The furious ambassador reveals that the virus was concealed within his hover chair, and releases it into the citadel tower before flying away. Jacob warns everyone to escape, then takes on the ambassador's batarian troops and combat drones. After Jacob finally defeats Jath'Amon, he tells Jacob that they are not so different; as both of them are willing to go to great ends to protect their people. Jath'Amon swears revenge on Jacob and the Council as he is led away by Citadel Security.

After resuming his vacation on the Arcturian Jade, Jacob is watching a news report about Jath'Amon's arrest when he is surprised by a noise behind him. After grabbing his assault rifle, he realizes the intruder is Miranda, with a bottle of champagne and a smile.

Awakening
Commander Shepard awakens in the year 2185 aboard a Cerberus space station, a research facility of the Lazarus Project, which is under attack by hacked security mechs. After the Commander aids Cerberus agents Miranda Lawson and Jacob Taylor in escaping, Shepard is taken to a headquarters of Cerberus and granted an audience with the Illusive Man, who explains that Shepard was revived and "upgraded" in return for the Commander's aid in combating a new threat in which human colonies have been attacked, their colonists deemed missing.

Shepard and the team are dispatched to investigate the recently attacked colony of Freedom's Progress, located in the Terminus Systems. There, the group encounters Tali'Zorah vas Neema, one of Shepard's former squad members, and discovers that the mysterious insect-like Collectors were behind the attack and are responsible for the further abductions of other human colonies. Shepard reports this to the Illusive Man, who then places Shepard in command of the Normandy SR-2, a larger ship modeled after the original Normandy SR-1. With the guidance of the Illusive Man, Shepard begins traveling across the galaxy to recruit a new team for what is assumed to be a suicide mission.

Recruiting A Team
The Illusive Man initially provides Shepard with four dossiers regarding potential recruits: a salarian scientist, a mysterious vigilante called Archangel, a krogan warlord, and a powerful but psychotic biotic. The salarian, Mordin Solus, is found on Omega and is working to stop a plague engineered by the vorcha who are working for the Collectors. The vigilante Archangel is also on Omega, holding out on his own in a battle against three mercenary gangs. After reaching Archangel's hideout, Shepard learns that Archangel is actually Garrus Vakarian, one of Shepard's previous squad members. Garrus is seriously injured while battling the mercenaries, and, although he is permanently disfigured, he survives and joins the team. The krogan warlord, Okeer, is found attempting to create the perfect krogan through unethical genetic research. When the warlord is killed, he leaves his creation, Grunt, under the care of Shepard. The biotic, Jack, revealed to be a woman, is also known as "Subject Zero." Cerberus arranges for her to be purchased from the prison holding her; Shepard travels to the Purgatory prison ship. Once there, however, Shepard is betrayed by the warden as he attempts to capture Shepard for a bounty. Shepard manages to escape the trap and rescue Jack, who joins the team despite an initial distrust of Cerberus operatives.

After the recruitment of the four characters, the Illusive Man reveals that a human colony called Horizon has come under Collector attack, and he dispatches the team in an attempt to save the colony. He also notes that one of Shepard's surviving crew members, either Kaidan Alenko or Ashley Williams depending on choices made in the first game, is stationed at the colony to oversee the construction of massive defense towers. Shepard arrives with his/her team and battles the Collectors face-to-face; the group appears to have arrived too late as half of the colonists have already been taken away. Shepard later reunites with the former ally, who leaves feeling betrayed by Shepard working for Cerberus.

After returning to the Normandy, Shepard is provided with dossiers on three more potential recruits: an asari Justicar, a drell assassin, and Tali. Shepard finds the Justicar, Samara, on Illium. She joins the team after Shepard investigates the Eclipse mercenary group and its involvement in a murder. The drell assassin, Thane Krios, is also found on Illium and is in the midst of completing an assassination contract on Nassana Dantius. After learning of Thane's next target, Shepard fights resistances along the way to the top floor of the tower complex where the target is located. Shepard encounters Thane, who successfully dispatches his target and joins the team, as Shepard can provide him with a purpose. Tali is found on a geth-occupied quarian colony world, Haestrom, where she is researching the system's rapidly dying sun. After she is rescued from an immense geth force, she agrees to join Shepard.

Collector Ship
The Illusive Man informs Shepard that a turian patrol engaged a Collector ship, and managed to disable it before being destroyed, and that the Normandy should take the opportunity to investigate the ship before the Turians respond, and find any data or technology that can help them on their mission. Upon boarding the ship, Shepard discovers many empty collector pods, as well as the bodies of dead human colonists, apparently subjected to various experiments by the Collectors. Shepard then discovers that the Collectors had also been experimenting on their own, with EDI saying that they appeared to be researching their own genetic similarity to humans. EDI's genetic analysis of the deceased Collectors reveals that they are in fact the long extinct Protheans, having been subjected to extensive genetic modification to alter them for the Reaper's purposes.

As Shepard proceeds deeper into the ship, Joker discovers that it is in fact the exact same Collector vessel responsible for the attack on Horizon and the destruction of the original Normandy, which Shepard remarks is far too uncanny to be coincidence. When Shepard's team reaches the center of the ship, they discover that it contains millions of empty pods, more than enough to hold every human in the Terminus Systems, thus indicating that their ultimate target must be Earth. Shepard is able to link EDI with the Collector ship's systems in order to search for any useful information, but she is quickly interrupted as she discovers that the ship is not disabled, and the Collectors have drawn the Normandy into a trap. Shepard and crew fight their way out and escape from the ship on the Normandy before the Collector vessel can bring its weapons to bear. After escaping, Shepard speaks with the Illusive Man, who admits to sending the Normandy into an obvious trap in order to gain information, and says the data gathered by EDI has led to the discovery of the Collector's means of traversing the Omega 4 Relay, a Reaper IFF. EDI is also able to calculate the location of the Collector homeworld from their ship's navigational data, and reveals it to be within the galactic core, an extremely dangerous area, which likely accounts for the fact that no ships ever return from the other side of the Omega 4 Relay.

The Key
The Illusive Man then reveals that the Omega-4 relay - beyond which lies the Collector base - requires a piece of Reaper technology in order for the Normandy to successfully navigate through it. It is revealed that Cerberus had located a derelict Reaper, evidently destroyed millions of years beforehand, and sent a science team there to recover the required device - an IFF transponder. During the course of the investigation, Shepard discovers that the Cerberus science team members had all been killed before their arrival. Battling their through the Husks on board, Shepard and the team recovers the IFF and salvage a damaged, but friendly geth before destroying the core of the ship. Following the mission, Shepard may choose to either turn the geth over to Cerberus for research or activate it. If activated, the geth will be named Legion by EDI and joins the team against the Collectors.

Shortly after, Shepard departs with the recruited members on a shuttle towards their next mission as the Normandy prepares the IFF for testing in their absence. A hidden signal is found, however, after the activation of the IFF, and Collectors ambush and board the Normandy. Joker is forced to give control of the ship over to its onboard A.I., EDI - a potentially dangerous move. After successfully gaining control of the ship, EDI manages to pilot the Normandy away from the Collectors and rid the ship of all enemies, but the entire crew barring Joker is taken. Upon returning to the ship, Shepard's hand is forced - the Commander can either continue completing secondary missions and sacrifice the captured crew, or to go through the Omega-4 relay immediately to rescue the Normandy crew members.

Beyond the Relay
After traveling through the relay, the game may proceed in several ways due to several factors. Depending on whether or not Shepard enters the Omega-4 relay quickly, has upgraded parts of the Normandy, and has earned the the loyalty of team members, any combination of crew and team may survive or perish during the final mission, including Shepard. Regardless, Shepard and the team battle their way to the core of the Collector space station. There, they discover that the Collectors have been constructing a new human-like Reaper, made from the genetic material of the abducted humans and fused with the advanced technology of the Reapers. Shepard targets the weak structural points of the contraption, which is in the early stages of its construction, and it is seen collapsing into the lower confines of the area.

At this point, the Illusive Man contacts Shepard and suggests to keep the station intact to allow research on its technology, under the pretense that any garnered information would be valuable in the coming war against the Reapers. Shepard may choose to either disregard the Illusive Man's advice and destroy the station or use a radiation pulse to kill all surviving Collectors thus allowing Cerberus to take control of the station. If Shepard chooses to destroy the station, and Miranda is with the Commander, Miranda may choose to resign from Cerberus, depending on her loyalty to Shepard. After Shepard and the team destroy the Reaper, the surviving squad members escape to the Normandy and leave. A final cinematic shows the Normandy undergoing repairs following the mission and concluding with the Reapers awakening from their hibernation in dark space.