Mass Effect 2 Guide

This page contains a walkthrough for the main missions of Mass Effect 2. Major changes in the gameplay from Mass Effect are listed in the main Mass Effect 2 page, while the effects of importing a saved game from Mass Effect are listed in the Save File Transfer page.

Save Joker
The SSV Normandy SR-1 is under attack from an unknown enemy. The ship is taking catastrophic damage and the crew have begun evacuating. A member of the crew, either Kaidan Alenko, Ashley Williams or Liara T'Soni (based upon your romance choices from an imported character or the gender of a new character), informs you, Commander Shepard, that the ship's pilot, Joker, is reluctant to leave. After you convince Kaidan/Ashley/Liara they must abandon ship and save the crew, you are tasked with convincing Joker to leave.

As you gain control of Shepard, walk through the blazing hallways keeping to either the left or right and up a set of stairs where you will reach the doors to the damaged Command Deck, now exposed to open space as the roof has completely disintegrated. Walk forwards towards the cockpit, eventually reaching a kinetic airlock where you will find Joker reluctantly giving up against extremely unlikely odds.

A cutscene begins as you carry Joker into an escape pod. Before you can enter the pod, an energy beam and the resulting blast separates you, forcing you to eject Joker by himself. Another explosion sends you flying into open space where you soon realize your suit is quickly losing air. You struggle for a brief moment before losing consciousness, your body falling into the nearby planet's atmosphere.

Awakening
After the opening credits, which show you being literally "rebuilt" by the Lazarus Project, you awake on a laboratory table to the sound of the station alarm. Miranda Lawson will introduce herself over the radio and give Shepard instructions.

Walk to the locker to obtain a pistol and armor. Use the cover command to avoid damage from the explosive, then continue on through the open door into the next room. Take cover behind the crates and quickly pick off the lone LOKI Mech on the stairway.

Proceed through the next few rooms, where you will encounter a few LOKI Mechs; they will be the some of the easiest targets you will find in this game, and Overload/AI Hacking will make this easier if you are on a harder difficulty setting. It might be a good idea to knock them down and kill them for the Brawler achievement.

Along the way, you will find various recordings by Miranda and Dr. Wilson about their experience reviving Shepard. You will encounter some items you can investigate, where you are introduced to the hacking and routing mini-games (which replace the previous 'manual override' game from Mass Effect). As this is the introductory Prologue, you are allowed to retry the mini-games indefinitely until you succeed.

Eventually you will meet Jacob Taylor. There will be a brief dialogue, which Jacob will cut short so that you can clear out some mechs.

 Note:  If you do not follow the on-screen suggestion to use Jacob's biotic abilities, the enemies will keep re-spawning until you deign to do so.

After clearing the room and speaking further with Jacob, the two of you will continue through the facility until you meet up with Miranda's assistant, Wilson, who is injured. You must obtain a medi-gel from the first aid station, and use the Unity ability to heal him. After some dialog, all three of you will head toward the shuttle bay where more enemies await you. There is also a datapad in this area, which you can hack. The mission ends when you arrive at the shuttle bay and meet with Miranda.

Freedom's Progress
The Illusive Man sends you to Freedom's Progress, the most recent colony to disappear. Commander Shepard's mission is to recover any clues or information as to who is responsible, with help from new found squadmates Jacob Taylor and Miranda Lawson.

On arrival, proceed through the door and make your way through the colony, killing any LOKI mechs and FENRIS mechs that you encounter. Watch out for the one LOKI mech that is folded up inside one of the colony buildings, next to a locked wall safe.

Eventually, your squad will run into and confront Tali'Zorah nar Rayya and a group of quarians led by Prazza, all of whom express great distrust for Cerberus. Tali explains that their mission is to find Veetor, an unstable and sensitive quarian who came to the colony on Pilgrimage. They suspect that Veetor, nervous to begin with, must have suffered damage to his suit during the attack, the subsequent infection causing him to become paranoid and reprogram the security mechs. The two squads decide to work together to find him.

Continue through the door, noting the combat drones that fly past your squad, and enter the next area through the gates. Here, the mixed group of Assault Drones and Rocket Drones will attack your team. Use Miranda's Overload ability to cause the drones severe damage, and stay behind cover in order to avoid the enemy rockets. Continue to move forward.

Eventually, Tali will contact you saying that the other quarians went on ahead, despite her protestations, in an attempt to locate and remove Veetor before Shepard can question him. Proceed to the large gate and order your squad mates to take cover on either side of it, then hide yourself behind the obstruction in front of the entrance. Once in position, Tali will open the door remotely.

A YMIR Mech takes out the entire quarian team, then turns its attention to you. The mech is protected by shields and armor, and is equipped with a rocket launcher and machine gun. Do not expose yourself – its weapons can incapacitate you within seconds. Also, move from one piece of cover to the next, as the mech will destroy cover throughout the battle. The YMIR advances on your position and may flank you if caught off guard. Once destroyed, scan the mech debris in front of the objective building for a heavy weapons upgrade, and check the buildings on either side for items and credits.

Finish the mission by finding Veetor, who is babbling in a paranoid manner about monsters out to get him, and watching garbled footage on a wall of display screens. Shepard will have a Renegade interrupt option, followed by a Paragon interrupt, in order to get Veetor's attention. Tali walks in shortly afterward. Veetor, though delirious, has managed to piece together footage from the colony's security cameras to reveal that the Collectors are behind the abductions. The group theorizes that Veetor was spared because the Collectors are only scanning for human vital signs, or are only interested in humans. Miranda will insist that the quarian be taken into custody for interrogation, but Tali insists he be taken back to the Flotilla for medical attention. The final decision rests with Shepard, after which the mission ends.

 Note: If Veetor is allowed to return to the Flotilla, he has the option to testify on Tali's behalf later during her loyalty mission''. ''

The Professor
It is a good idea to follow Miranda's advice and recruit Mordin first. Recruiting Mordin unlocks the Normandy's Tech Lab, allowing the player to upgrade their equipment (which can then be used on all subsequent missions). Head to Omega and speak with Aria T'Loak in Afterlife about Mordin and the plague spreading through the slums (it is also a good idea to speak with her about Archangel now and talk to the mercenary recruiter in order to save time later. See "Archangel" below). Proceed to the markets section of Omega and then talk to the turian guard who is responsible for enforcing the quarantine just before the markets. He will allow you to enter the slums.

Upon reaching the slums, fight your way through the Blue Suns mercenaries. You can talk to a dying batarian civilian; a Paragon interrupt will keep him alive long enough for Mordin's assistants to help him later. Letting him die, however, nets you 2000 credits from a datapad. Bypassing locked doors will allow you into apartments, some of which contain refined resources, and one of which houses a pair of human refugees. Talk to the refugee couple and select either the paragon or renegade speech options to convince them to head for Mordin's lab. Otherwise, the path to Mordin's lab is rather straightforward.

After you have reached the clinic, talk to Mordin. He will ask you to insert the plague cure into the ventilation systems, and then re-activate life support, he will also give you a second heavy pistol that will stay in your weapon inventory. Head out the unlocked door and make sure to enter all doors. You will find Mordin's assistant being threatened by a group of batarians; resolve the situation as you will and continue to the environmental controls.

Upon arrival, a vorcha reveals that the Collectors are behind the plague. Once there, follow EDI's instructions to place the cure in the console in the center platform. Then go to the east and west fan controls, fighting more Blood Pack vorcha and krogan on the way. After you activate both fans the mission is over and you are back in Mordin's office, ready to return to the Normandy. Make sure to gather all the items available in the clinic, including large amounts of refined resources. If you saved the batarian civilian and/or talked to the refugee couple, they will be waiting in the clinic, and will express their gratitude to Shepard if talked to.

Note: Attempting to bring either Grunt or Garrus into the quarantine zone triggers dialogue regarding the effects of the plague on the squad member, and you can choose to send him back to the Normandy when entering the quarantine area. If you keep either squad member with you, he mentions feeling sick along the way to the clinic but Mordin treats him upon arrival.

Archangel
Archangel is found on Omega. After you acquire information from Aria T'Loak in Afterlife (she is expecting you) about joining a mercenary group, you may sign up to "takedown" Archangel. To do this, go into the the private room in Afterlife (this will be directly to your left when you enter the club). You have to apply for a freelance spot to attack Archangel. Once you're done applying, you'll start to walk out, passing a young-looking, gun-wielding man. You will overhear him ask about applying to fight. At that point, an opportunity for a Paragon interrupt appears. If you take it, you'll disable the cheap pistol and walk out of the room (If you do this, you'll later get a private message from the teen at your private terminal on the Normandy, thanking you from stopping him). Exiting the club, there is a small alcove with vehicles that look very much like Citadel Rapid Transport vehicles in it. A batarian wearing Blue Suns armor is standing guard. When you're ready, you may speak with him, and he'll take you to Archangel's base (It is highly suggested that you prepare yourself well for the Archangel mission, as once you get to Archangel's base, there is no returning until the mission ends).

You will then be transported into a mercenary encampment, where you can talk to several of the mercenary leaders and gain valuable insight into their operations. As you make your way through the hallways, check for footlockers containing cash and raw materials. In addition, you will be given the opportunity to disable/sabotage the YMIR Mech and/or A-61 Mantis Gunship. The YMIR Mech is located in a small room off to the side containing a console which can be hacked. Later, Shepard will talk to a mechanic repairing the Gunship; at the end of the conversation a Renegade interrupt opportunity will allow Shepard to incapacitate the mechanic. Do both to make the upcoming battle much easier. However, shortly after you do this, you will be ordered to begin your assault. Your assault requires you to run across an open bridge as Archangel picks off your freelancer companions one by one. After making it across the bridge, you confront Archangel. He removes his helmet and reveals himself to be Garrus.

After a small discussion over events to occur, the mercenaries begin their assault. Shepard and the Commander's team have to defend Garrus and his position from waves of mercs, including a YMIR Mech. If the YMIR Mech was sabotaged earlier, it will attack the mercenary enemies. After a few waves are cut down, the mercenaries begin drilling their way through the sealed passageways below. Shepard takes the team below ground to reach three sets of blast doors in order to lock them off for good. It is advisable to lock the doors as quickly as possible, as never ending waves of enemies will rush through the doors until their closed. After a long firefight, Shepard goes back up stairs where the mercenaries are preparing for their final assault. Next you have to fight a Krogan Battlemaster known as Garm.

He is quite difficult to handle at close range but there is a glitch when fighting him. As soon as the clip ends and you're able to move, run straight over to Garm and up the stairs to Garrus. If you are in front of Garm, he will not have his weapon out until he reaches Garrus' room. you can easily kill him before he even gets to shoot at you or Garrus, making this part a piece of cake.

After defeating Garm, the fighting stops, and Garrus recommends making a break for it across the bridge. Just as you are about to leave, the A-61 Mantis Gunship appears, guns down Garrus and drops off more mercenaries. If the mechanic was incapacitated earlier, the Gunship will be at half health. Winning the fight is tough, but with enough tech and biotic abilities, Shepard will prevail. Use all the tools at your disposal; incendiary and armor-piercing ammo will help. As you run towards Garrus' lifeless body, he begins to wake up. You return to the Normandy. The conversation with Garrus afterwards reveals that his face was badly damaged; scars run along the right side of his face, along with a large bandage/dressing which will stay with him throughout the rest of the game. Despite his wounds, he is no worse for wear and is ready to help Shepard fight the Collectors.

For special additional dialogue, acquire Grunt first and bring him along, and then talk to Garm, the leader of the Blood Pack mercenary gang, before engaging in the mission proper. Picking the right dialogue options results in Garm taking out a gun and blasting the head off the vorcha standing next to him.

Similarly, taking Zaeed will enable additional dialogue when you speak to the leader of the Blue Suns before the mission.

The Convict
Jack (referred to as Subject Zero) is found on the prison ship Purgatory. Once the player arrives at Purgatory, they meet the Warden, who claims that his job is to keep the galaxy clean from criminals. However, you quickly learn that he is only interested in selling the criminals for personal gain and attempts to capture Shepard. Since you are fighting blue sun mercs, overload is very useful for this mission (especially on insane) as most of the enemies have shields

You will be ambushed by a group of mercs and fenris mechs with only one way out. Fight your way out of the ambush, and activate the console in the next room. Jack is released from her cell, and proceeds to wreak havoc on the station. Move from cell-block to cell-block, stopping to fight enemies whenever necessary. Most enemies are Blue Suns mercenaries, backed up by LOKI Mechs and YMIR Mechs.

The final firefight involves the Warden, who is protected by three force-field generators. The generators are situated throughout the room and protected by Blue Suns Legionnaires, Soldiers, and Commanders. Destroy all three generators quickly and focus your fire on the Warden, as once he falls the battle is over. There will be an unlimited amount of enemies until you kill him. Afterwards, Shepard tracks down Jack, who is originally hostile to Cerberus; however, Shepard convinces her to join them.

The Warlord
The Warlord (Dr. Okeer) is found at Korlus in the Imir system. Right after a flight in the Kodiak Drop Shuttle there will be a short cut scene. Head down around the corner and be ready to shoot some Blue Suns troopers, enemies count at three. After that, go on and you will have to talk to the wounded mercenary, after getting information on The Warlord continue down the road. Enemies will be waiting for your on top of the ship deck. Two on the front port, two on the bridge and two on the far bridge. There is also a med-kit. Again continuing down and up the stairs there will be more enemies coming. But now there will be Blue sun Heavy (using the ML-77 Missile Launcher) – total heavy count at three.

Continue down, there will be a Tank-Grown krogan to talk to, before being able to talk to him, there will be five easy enemies to kill. Now there will be a cut scene talking to him, getting more information about The Warlord, after that the tank-grown krogan will move the metal plate blocking the way down. There will also be a Blue Sun corpse to access (+2000 credits). Continue downhill there will two enemies running away from Krogan Berserkers, they will pop out very suddenly so be careful. Now, there will be a long fight, more krogan berserkers will come after you. There should be a med-kit around, after the fight go on towards the stairs. There will be a loot on Refined Platinum (+2000 Platinum). You will have to bypass the door upstairs. Continue upstairs, now there will be power cells, medical station and a sniper rifle upgrade.

Opening the door will make you go into another fight, enemies count at 4 and 1 heavy. Continue down the hallway, there will be enemies waiting for you. After the fight go towards the door, before continuing, to the right side of the door there will be a PDA (+4000 Credits) if you hack it successfully. Going upstairs again there will be another fight. There will be a med-kit to the left side of the door on the table. After the fight, a Blue Sun corpse will be accessible (+2000 Credits). Again there will be another fight, after the fight inside the room there will be power cells and a wall safe (+4000 Credits). Continue down the hallway, do not enter the door yet. There will be a PDA (+4000 Credits) if you go on the hallway. After this fight, there will be a cut scene where you meet with Rana Thanoptis from Virmire, provided that you imported a ME1 save where she survived. Inside the room, there will be a medical station and a secure terminal (+4000 Credits), and after the cut scene there will be another cut scene after talking to Dr. Okeer. Before continuing there will be a lab terminal (upgrades Krogan Vitality by 25%).

Now the fun kicks in, there will be a miniboss fight, Jedore, and her “army” of krogans and an few YMIR Mechs. Three sniper headshots should kill Jedore if you are a Soldier or an Infiltrator in normal difficult. In hardcore difficulty, four headshots are required with the upgraded bolt action rifle. Killing Jedore will stop any remaining krogans from being released to fight you. You may also set your team up in the back room (where you came down the ramp); you will be able to walk into the room and trigger the release of a Krogan. You may then retreat up to the first landing and wait for the Krogan to walk directly into your line of fire. Make sure you have a lot of Biotic/Tech to use in order to stop each one from shooting you and killing you too quickly. When this was tried last, there were four Krogan released, and then no more were ever sent out of the tubes. Then the player was able to duck behind the guardrail just inside the door and whittle away at the YMIR Mech, without taking any damage (or using any ammo, for that matter. Stealth and Incinerate were great helps in that).

The Veteran (DLC)
Zaeed Massani is found on Omega. After completing your first mission on Freedom's Progress, the Illusive Man will tell you to go to Omega to find Mordin Solus, Zaeed Massani will be found right outside the docking area along the passage way. Zaeed Massani will join your squad after you talk to him. He will also inform you of a his mission he hadn't completed. Completing the mission he informs you of will gain you his loyalty.

Over the Horizon
Mission Walkthrough: Horizon (mission)

A short cutscene shows Kaidan Alenko or Ashley Williams (depending on who survived Virmire in the original Mass Effect, or Shepard's gender if a Mass Effect save was not carried over) and other Alliance soldiers speaking and working with colonists. A strange ship (later revealed to be the Collectors) attacks the colony. This is Shepard's first encounter in the game with the Collectors.

Ignore the "frozen" humans (you can't interact with them) and fight groups of Collectors to the end of the map. Make sure to pick up the Collector Particle Beam heavy weapon. Shepard will eventually reach a garage, where a mechanic tells you what happened. Use the Weapons Locker to select your desired output, and then proceed out the opposite door.

Shepard's squad must now activate the uplink and hold the area against enemy forces in order to buy time for EDI to activate the large cannons and drive the Collector ship away. Enemies include waves of Husks, Collector enemies (including Harbinger), and Scions.

The final enemy is a lone Praetorian, which may pose a challenge at higher difficulty levels. The Praetorian will attack with an energy beam weapon while moving towards Shepard. Take cover to avoid the beam as soon as it begins firing, as even brief exposure to the beam will severely damage Shepard's health and shields. When wounded and in close proximity to Shepard or another squad member, the Praetorian will slam the ground, sending out a shockwave and stunning any party member in close proximity, while activating a biotic barrier. In most cases, the Praetorian will focus on Shepard, giving the other squad members ample opportunity to attack the enemy.

After the Collectors have been driven away, there is a dialogue scene with Kaidan/Ashley. If Kaidan/Ashley was Shepard's romantic partner in Mass Effect, there will be additional dialogue.

The Assassin
On Illium, go see old shipmate Liara T'Soni, now a full time information broker. Liara will direct you to another asari woman, who will then transport you to a construction site where Thane has an assassination target. It is a good idea to search the tower as there are trapped salarians who offer Paragon/Renegade interrupts. Throughout the tower, you will encounter Eclipse troops and mechs; Eclipse troops are fond of techs and rocket launchers, preparing for long/mid ranged fights is a good idea. Fight your way to the top of the towers and across the skybridge to find Thane's target. When you get there, a short conversation ensues before Thane drops in and kills everyone. Mission accomplished.

The Justicar
While on Illium, talk to Liara. She'll give you directions to speak with an Asari in the transportation section, who will direct you to catch a cab. You will end up outside of a murder scene, talk to the asari cop in the station to get permission to enter the crime scene. After taking down a few lightweight mercs you will go to a cutscene showing the Justicar (Samara) making easy work of some Eclipse mercs. Unfortunately she's tied up with the pressing issue of finding a ship, on top of that she is a wanted "woman" by the cops, who take her into custody. However, she will join you, and the cops will release her into your custody, if you find the aforementioned ship name, which sounds easy enough. Talk to the volus, Pitne For, either by stroking his ego (paragon), or convincing him with your pistol (renegade) as to what he knows about the present situation in regards to the ship. Open the previously locked door, and prepare for multiple firefights.

In a hackable door on the right, there will be an Eclipse merc who just so happens to be "innocent" in all this hoopla going on. A quick renegade interruption will get her to screw up her current story and put into early retirement (you will find out who she was later in the mission). Make your way through more firefights followed by a shootout with a gunship. The gunship will flank your cover positions so it is best to draw its fire then go back and take cover near the entrance to this section where the gunship can only attack from your front. Towards the end you will participate in a rather comical scene with a "high" volus, who wants to kill Captain Wasea (the Eclipse boss), you can let him try (renegade) or get him to sleep off his buzz (paragon). After killing Captain Wasea be sure to loot the area for credits and resources, and get the name of the ship so you can add Samara to your squad.

Tali
Go to Haestrom, which will be available after completing the Horizon mission. Tali'Zorah nar Rayya and her mission team is on the planet when geth arrived and lay siege on them. The objective is simple: clear your path towards Tali by going through swarms of geth. To complicate matters further, the unstable sun is giving off large amounts of radiation that will bring down your shields within seconds in direct sunlight. This forces the player to leap-frog between shady areas and remain in cover.

Go down to the small bunker where there is a console to open the gates. Once inside, a geth dropship will drop several geth that need to be defeated. It is advised to avoid the bridge in broad sunlight and instead, make your way diagonally across the area to a shadowed stairway where there is a weapon upgrade on a dead quarian. Go through a few doors and corridors, paying attention to scannable upgrades on dead geth, and find a com-link to speak with Captain Kal'Reegar, leader of the military squad protecting Tali, who provides you status updates. Just ahead, you will see a squad of defending quarians killed by an attacking geth dropship and causing a pillar to collapse on them and blocking your next path. EDI will inform you that you need to find two explosive charges to blow the rubble away. Acquire the charges from two bunkers, while taking out 4 waves of geth, and set them on the rubble and take cover. You will arrive in a room where you will find several credits, a weapon upgrade. Communicate through a com-link to ask Tali to open the doors to proceed.

Make your way through another area where there are multiple geth probes which can cloak, not so annoying as the Geth Prime in the area so stay take cover (and out of the sunlight). Make your way into the next bunker and open the shutters where a Geth Colossus welcomes you to the party. Going down a stairwell, you will meet Kal'Reegar who informs you that Tali is on the other side, locked in and you have to defeat the Colossus and the other geth to get to her.

Kal'Reegar offers to distract the Geth Colossus to allow Shepard and team to head closer to the Colossus. At this point, you have the option to do a paragon interrupt and decline Kal'Reegar's offer, thus keeping him out of battle and surviving the Colossus' attacks. If you choose not to interrupt and you accept his assistance, there's a possibility of him dying in the process. If he survives, he is able to speak on Tali's behalf in her (loyalty mission) trial.

You are advised to use any tech skills against the Colossus along with heavy weapons. Keep watch of your flanks as geth will attack you from any position. Sticking to the far left or right path instead of down the middle of the area can help avoid this.

After you defeat the geth, Tali opens the door for you. She explains that she is on a mission for the Migrant Fleet to examine and collect data on the system's prematurely aging sun. Unlike your first encounter, you are now able to recruit her to your squad.

 Note:  If this mission is played under "Hardcore" or "Insane" difficulty (the difficulty setting must be set before the mission), you will find a Geth Pulse Rifle in the room where Tali is in.

Collector Ship
 IMPORTANT NOTE:  This mission has been known to trigger after recruiting only one of the crew members made available in this chapter. This most likely is caused by having the Zaeed DLC. It can be surmised that it triggers upon having 6 crew members in total and having performed a certain number of missions or assignments.

After recruiting two of those crew members, you must board a disabled Collector ship at the request of the Illusive Man, who contacts you with information regarding a turian cruiser engaging the Collectors. The turian ship was destroyed, but managed to disable it, supposedly due to the additional damage the ship received from the Alliance turrets back on Horizon.

After boarding the seemingly empty Collector ship, you will come to a pile of dead humans, which sparks a conversation as to why the Collectors are taking humans as captives. You then find a deceased Collector with evidence of it having being operated and experimented on. Another conversation between squad mates and EDI reveal that the Collectors are in fact the long-lost Protheans, twisted and forcefully adapted to serve the Reapers as mere tools. After the conversation ends, you will find a pile of weapons next to the console; the game gives the player the option of either training in a weapon that they are unable to use normally, or alternatively, the player may choose to select an upgraded weapon for a weapon proficiency that they already have. There are 3 of them you can choose from, but can only receive the advanced training to operate one. The three choices are: the M-300 Claymore Heavy Shotgun, the M-76 Revenant light machine gun, or the Widow Anti-Material Rifle. The weapon chosen must have the basic training associated with its class, e.g. the M-76 Revenant requires the ability to use assault rifles, thus only soldiers can select it. It is not possible to have all three for Shepard, even across multiple playthroughs. In case of playing with a class with no access to either shotguns, assault rifles or sniper rifles, such as an Adept or Sentinel, picking any of those gives you access to the basic training for that weapon but not the special gun. Don't forget to make a stop at the weapon locker and the heavy weapon ammo crate a short ways after the weapon pile.

After proceeding further, Joker and EDI will attempt to scan the Collector ship only to find out you've been lured into a trap (which the Illusive Man was quite aware of). Make your way to the console on the platform so that EDI can buy time for you to get off the ship before the Collectors activate their weapons systems. Defeat the Collector waves incoming on multiple platforms then reactivate the console. Avoid the temptation to use your heavy weapon and save it for the Praetorian. You will have to fight your way back to the shuttle through waves of Drones, Harbingers, Husks, a Scion and a Praetorian, be sure to look for various upgrades on your way out.

Reaper IFF
 IMPORTANT NOTE:  It is strongly recommended to delay this mission until you have completed all character specific conversations, loyalty side missions, and weapon/armor/ship upgrades, in order to ensure max survivability (your team and the entire Normandy crew), since you will most likely only be able to squeeze out one more mission (which should be Legion's loyalty mission) prior to making a choice to enter the Omega-4 relay. If and only if you unlock Legion's loyalty mission before going to the galaxy map after this mission then you have some time otherwise you will go right to the ambush.

Shepard is tasked with investigating a derelict Reaper orbiting the planet of Mnemosyne and locating a Reaper IFF system which should allow the Normandy SR-2 to safely enter the Omega-4 relay. Unfortunately, Cerberus has lost contact with the science team it dispatched to the Reaper earlier.

This mission will pit you against Husks, Abominations and a few Scions. It is advisable to bring at least one team-mate with a shotgun for this mission; Incinerate, Area Pull and Slam are also useful skills – Incinerate is an area of effect power which can easily bring down the Husks and Abominations' weak armor, and after that, using high-level Pull or Slam will instantly kill them. The upgrades which increase Shepard's resistance to melee attacks and melee damage are also useful. Groups of explosive crates indicate an ambush.

A good strategy is to place squad-mates at the near end of one of the many long corridors within the Reaper, preferably upon higher ground, and then trigger a wave of enemies by running forwards. After the enemies appear, retreating to wherever your squad was waiting allows for them to land many free shots upon the enemies while they attempt to close the distance. It is important to stay out of cover and avoid being cornered or surrounded by Husks.

After entering the ship itself, Joker will inform Shepard that the Reaper has reactivated its shields. The mass effect core of the Reaper must be destroyed to disable the kinetic barriers and allow the squad to leave the Reaper. As you are advancing toward the core, a cutscene will trigger showing a single geth soldier with N7 armor killing a few husks around you. The squad will then fight their way to the actual core where the geth will be knocked out by husks. The players job from here on is to destroy the glowing blue mass effect core while fighting off infinite waves of husks. The glowing blue mass appears after its shields are retracted (roughly every 30 seconds). Missiles are strangely misdirected by the core and firing one will result in the missile flying to the left or right. The best tactic is just to save enough heavy weapons' ammo for one M-920 Cain shot, prepare the weapon just after getting the Reaper IFF and before entering the core room, and shoot it just after the cutscene, while the core is still open. This will make a 1-hit KO.

Activating the IFF
The IFF will be integrated into the Normandy in order to allow transit through the Omega 4 relay. As part of this procedure, the IFF must be thoroughly tested. Once the IFF is ready to be activated and tested, Joker will inform you that the crew should use the shuttle for the next mission.

While Shepard and the commander's team are gone, Joker and EDI will discuss the Reaper IFF. EDI informs Joker that she has detected a hidden signal being transmitted by the IFF which may give away the Normandy's location. Before Joker has a chance to stop the integration, a Collector Cruiser jumps in right on top of the Normandy and Collectors begin boarding the ship. Joker is unable to control the Normandy due to a virus which has locked up the ship's systems.

The only way to escape is for Joker to release EDI's control lock and give her command of the ship by connecting her systems directly to the ship's control systems. The player then takes control of Joker. Have Joker hobble to the Tech Lab (follow the lights on the floor), and then to the AI Core via a maintenance shaft. As you move, Collectors will appear and engage in combat with members of the crew or drag them away. You should be able to make it just by moving quickly and not stopping.

Next, EDI will need you to go to Engineering and restart the core. This is a little trickier, since there are Collectors in your way. If you rush up the stairs, Joker will be spotted by a Scion or Praetorian, and the mission will end in failure. Instead, move to the stairs and wait until EDI tells you that the corridor is clear before entering Engineering. Activate the console to restart the core.

When the core comes back on-line, EDI will have full control of the Normandy. After she clears the ship of Collectors by opening all of the airlocks (except for the sealed engine room), the Normandy will jump away; leaving Joker the only crew member remaining on board. After Shepard returns, he/she has a decision to make. Either head straight to the Omega 4 relay, or complete more missions: Either way, the actions above will have no impact on the No One Left Behind achievement and you will get a short gory cutscene.
 * If you do not enter the relay immediately and continue to do other assignments, Kelly Chambers and all members of the crew will die in the Collector base and Doctor Chakwas will be the only survivor.
 * If you do between 1 or 2 assignments after the Collector's attack, about half of the crew including Kelly and Gabby will die. However, Doctor Chakwas, Ken and some unnamed crewmen will survive.
 * If you enter the relay immediately, only Lilith (a colonist from Horizon) will die instead. This holds true as long as you do no assignments after the Collector attack.  (e.g. you said you will delay the final mission, but you do it right away anyways.)

Interlude
This material is optional but will affect the final outcome of the game.

Upgrading the Normandy
Before reaching the end of this section of the game, you may want to upgrade your ship. The important upgrades are the shields, the armor, and the cannon. Tali, Jacob, and Garrus, respectively, provide these upgrades. For each of these you do not upgrade, you will later lose one team member. The upgrades also determine who dies and when. In order to protect your crew, purchase these upgrade before entering the Omega 4 relay.


 * Armor: Jack, Jacob, or Thane. An Oculus energy beam penetrates the Normandy's hull and instantly kills the crew member.
 * Shields: Tali, Legion, Thane, or Garrus. Tali and Legion are the 'preferred' victims; one is chosen at random. If both are not available because they are fighting the Oculus or Legion was not recruited, Thane or Garrus will die. They are vaporized when the Normandy's engine core explodes.
 * Cannons: Tali, Legion, Garrus, or Thane. You lose a party member when the Collector ship attacks you. The party member is impaled by a beam when the explosion of the Collector ship damages the Normandy. If Tali and Legion are in your squad fighting the Oculus, Garrus will die.

Note on Loyalty Missions
Each character you acquire for your party has a corresponding 'loyalty mission'. Successfully completing a party member's loyalty mission gains his or her loyalty resulting in an unlocked fourth power and an alternative costume for the member.

Loyalty missions become available as the game is played. Yeoman Chambers will remark to the player that a character wishes to speak with Shepard, and the loyalty quest will be added to Shepard's quest list. Talk to the character in question and agree to solve his, her, or its problem. Loyalty quests require that the character in question be part of Shepard's squad for the duration of the quest.

The first wave of loyalty missions begins after the mission on Horizon is completed. Jacob and Miranda's loyalty missions will be the first to become available. The following missions become available sequentially; each is unlocked after completing one mission with an 'Illusive Man' debriefing screen: Jack, Mordin, Grunt, and Garrus. Zaeed's loyalty mission is available as soon as he is recruited.

There are two situations in which loyalty can be lost. If this happens, the loyalty level of the character will be reset to 'normal', but the alternate costume and fourth power remain. Both situations can be resolved (in an identical manner) in a way that does not cause any loss of loyalty, but this requires a substantial Paragon or Renegade score. However, while loyalty can be restored, any potential romance for the affected character is permanently compromised.

Loyalty also influences character survival during the final mission. However, other variables will also play into whether all or some of your crew members stand with you in victory (such as the previously mentioned ship upgrades and team selection in the suicide mission described later in this article). Therefore, characters who are not loyal can also survive the game  if  they are not placed into compromised situations after proceeding through the Omega-4 relay.

Jack and Miranda
After completing both Jack and Miranda's loyalty missions (in either order), you will be summoned to Miranda's office in order to stop the two from fighting. Jack is angry that Miranda refuses to acknowledge Cerberus' mistreatment, while Miranda insists that the abuses which Jack suffered were committed by a rogue branch. A sufficiently high Paragon or Renegade score is required to keep both squad members' loyalty; taking one character's side will result in the other character losing her loyalty. If this does happen, a nearly maxed-out Paragon or Renegade score will allow the player to regain the squad member's loyalty through a conversation option later on [Confirmed: If you side with Jack, you can later convince Miranda with a signifigantly high enough paragon/renegade score. If you side with Miranda, you can later convince Jack that you were just paying lip service to Cerberus, you need a nearly full or full paragon/renegade to do so]. (On a side note, sometimes retraining powers to choose the option that gives you +100% on paragon/renegade can get you the extra p/r points you need, of course this only works if you had originally chosen the option giving +70%)

Tali and Legion
After completing both Tali and Legion's loyalty missions, you will be summoned to the AI Core in order to defuse a tense situation. Tali is angry that Legion is trying to send data about the quarian fleet back to the geth collective, and is threatening it with a pistol. Again, a sufficiently high Paragon or Renegade score is required to keep both squad members' loyalty. However, if the score is not high enough, siding with Tali and talking to Legion afterwards gives Shepard the chance to explain the actions with a lower score. Doing so will restore Legion's loyalty.

Garrus: Eye for an Eye
While on Omega, Garrus was betrayed by a member of his squad, named Sidonis, and sent on a wild goose chase while mercenaries killed his unit. Later on, Garrus receives intel that someone on the Citadel named Fade hid Sidonis. Once you arrive that the citadel, you meet with a volus pretending to be Fade. After a conversation with him, you learn that Fade is actually C-Sec officer Harkin, from Mass Effect. You then take the rapid-transit to the previously closed off Factory District, where you battle through mechs and Blue Sun forces to reach Harkin. After a confrontation with Harkin, he sets up a meeting between Shepard and Sidonis, at this point you have a chance to save Harkin from a angry Garrus or be renegade and let Garrus shoot him. During the meeting, you can either help Garrus and facilitate Sidonis's assassination, or inform Sidonis and spare his life. Allowing Garrus to take the shot and kill Sidonis gives a substantial number of Renegade points. Conversely, talking to Sidonis and preventing Garrus from taking the shot results in a substantial number of Paragon points as well as an explanation as to why Sidonis betrayed Garrus. However, as this action ends the mission immediately, there are no prompts to inform the player of exactly how many Paragon/Renegade points are earned by either choice.

Grunt: Rite of Passage
Prior to mission start, load up on your most powerful heavy weapon you have available; you will see why close to the end. Bring Grunt before the krogan clan leader on Tuchanka. If you kept Wrex alive in Mass Effect, he will be the clan leader, otherwise Urdnot Wreav will be the clan leader. After that, talk to the Shaman on the upper floor of the camp.

Grunt will be instructed to take a series of tests before a structure called the Keystone. The Rite of Passage consists of fending off three waves of enemies; each wave is triggered by activating the Keystone.
 * The first shockwave brings waves of varren, standard melee units.
 * The second shockwave brings klixen, which explode when killed and breathe fire at close range.
 * The third wave brings a thresher maw which shoots acid and burrows to one of three places roughly every 10 seconds. Any cover aside from concrete will break in one hit from the acid blast. To beat the final level, the player has two options. The first option is to wait out the five minute timer with the sole objective of surviving. The second option is to to kill the thresher maw within the time limit. Not a particularly daunting task, but you will unlock an achievement if you do (having the M-920 Cain will make this quick work).

Killing the thresher maw will trigger a scene involving another clan of krogan led by Gatatog Uvenk attempting to recruit Grunt. A fight will ensue against Uvenk and his krogan allies. Killing them ends the mission. (Note that there are two krogan bodies which can be looted during this fight, but they must be looted during the fight, as the mission ends as soon as the enemies are all dead.)

Jack: Subject Zero
Jack, being Jack, wants to blow stuff up! Specifically she wants to blow up the old Cerberus base on Pragia (Dakka System/Nubian Expanse) where she grew up. Of course, some mercs have other ideas and they'll try to get in your way. As you fight your way through them, hit all the conversation points and old computers to find out that the truth about Jack's childhood is a little different than she remembers it. Eventually you get to Jack's old cell, where you find Aresh, one of Jack's "classmates". He explains that, as bad as Jack had it, the other kids had it worse. Jack will either kill him or not. Afterwards, walk around Jack's cell and learn more about her experiences. Talk to her about the bed, window, desk, and old blood stain to learn more about Jack and end the mission.

Jacob: The Gift of Greatness
Jacob receives a message that he believes was sent by the Illusive Man. It informs him that a distress beacon signal from Jacob's father's ship, the MSV Hugo Gernsback, has been discovered after ten years.

Land upon the planet 2175 Aeia and proceed up the path, salvaging the spare parts. Listen to the log on the computer near the gangway, and then board the ship to listen to the other logs and to hack a PDA for credits. The V.I. beacon is nearby; talk to it to find out what happened to Jacob's father and the crew of the Hugo Gernsback after its crash. Continue on to find a 'survivor' cowering near a group of boxes. As the survivor tries to explain the situation to you, your crew will notice a group of armed men sneaking up behind the crates. Use the Paragon interrupt to save the woman from the Hunters, and then dispatch them. Note that the Hunters are unusually aggressive and will attempt to move on your position.

Follow the path ahead to the makeshift settlement, where Jacob will comment on the situation. Examine the spoiled food stores and the makeshift statue, and pick up the spare parts and the PDA for credits. A group of LOKI Mechs will move on your position; take them out and then talk to the doctor at the far end of the camp. She will hand Jacob a datapad detailing the actions of Jacob's father and the rest of the command staff. The path ahead is blocked by a barricade; hack the broken mech and move out of the way as it explodes and destroys the crates.

Continue onwards and take out the first wave of enemies: many LOKI Mechs, which will approach your squad from multiple directions. After you have destroyed the robots, make sure to scan the heavy pistol for the Heavy Pistol Damage upgrade, and continue along the path. The next wave of enemies consists of 'Brainwashed Guards', another LOKI Mech, and a YMIR Mech. The YMIR is the most dangerous enemy, as it will advance towards your position. Stay out of its line of fire; retreating down the path you took may buy you enough time to destroy the mech.

After dispatching all enemies, the door at the far end of the area will turn green. Proceed through the door to confront Jacob's father, who will try to justify his actions to Jacob (who is having none of it). Shepard can choose to secure Jacob's father for Alliance custody, to leave him stranded upon the planet with the Hunters, or to give him a pistol, which he will use to kill himself after the squad departs.

Legion: A House Divided
Legion will eventually inform you that geth actually are apathetic towards organics and those fighting organics are "heretics" following the Reapers or, as they call them, "The Old Machines". Legion will tell you that the heretics are developing a virus that will turn all geth into followers of the Reapers and asks you to head to an old, heretic-held quarian space station in order to destroy the virus threatening the peaceful geth.

The layout of the station is relatively linear. Several rooms will contain 'geth hubs' and inactive geth. Crossing the green circuit traces on the floor, shooting at the geth, or destroying the hub will result in the geth activating and attacking your squad. Destroy all hubs and geth in a room to stop the alarm and proceed. Note that destroyed hubs can be salvaged for 3000 credits each.

After the squad has reached the central computer core, Shepard can decide whether to reprogram the virus and use it to free the heretics from Reaper-control (Paragon) or to destroy it and the space station with all heretics on it (Renegade). If reprogramming is chosen, Legion will inform Shepard that the heretics will return to the geth and their memories incorporated.

Once Legion activates the console, waves of geth will activate and attack your position. The geth will try to make their way up the two staircases on either side of the room. There is a three-sided barrier between the console and the entrance to the room which makes an excellent position for your squad, allowing them to attack both waves of geth without exposing themselves to enemy fire. Geth waves consist of six units a wave, including geth troopers and geth hunters. Activate the rocket turrets at your discretion to make things easier; note that the turrets will self-destruct after a short period.

After you have fought off the geth, you will need to rush back to the Normandy. Exit through the now-unlocked door to the right of the terminal and fight through the geth. The final room contains a Geth Prime. Exit through the door to end the mission.

Miranda: The Prodigal
When Miranda escaped from her father, she also kidnapped from him her baby sister, a "twin" as she called her. Miranda then hid her from him on Illium. Her mission entails going to Illium and helping Miranda to move her sister and family to a new location. When you get there, you find that mercenaries have discovered her and you fight your way through them to meet up with Miranda's old friend, who you find has betrayed Miranda after learning that she had kidnapped her sister. He will tell Miranda that only he knows about her sister, her father has yet to be informed. Miranda will then shoot him although you have a Paragon option to stop her. After a final fight, you will find her sister unharmed and waiting with her family for a transport. Miranda will want to leave, although you have the option of convincing her to talk to her sister and letting her know she exists and loves her.

Mordin: Old Blood
On Tuchanka, one of Mordin's former STG associates has been "kidnapped" and Mordin asked you to save him. Talk to the "Scout Chief" in the Urdnot Camp. He'll lend you a truck to transport you to where Mordin's student is being held. Fight your way past the krogan and mercs until you find Mordin's old associate, who has not been kidnapped, but is instead riddled with guilt and working on a genophage cure. During the later half of the conversation, there will be a Paragon interrupt, which determines the fate of the student. Despite what happens to the student, Mordin defers the decision of what to do with the genophage research to Shepard. You may choose to destroy it or save it. After the confrontation, return to the Normandy, with Mordin's loyalty secured.

The choice presented regarding the destruction or preservation of the genophage research may or may not have an effect on Mass Effect 3.

Samara: The Ardat-Yakshi
Head to Omega and once again speak with Aria T'Loak about the Ardat-Yakshi. She will direct you to the apartment district (the door just before entering the quarantine area where you recruited Mordin) and check on one of Morinth's latest victims, a female human named Nef. Speak with Nef's grieving mother, after a short conversation with her, you are allowed to search Nef's apartment for evidence. Read her holo-journal's last entry to discover that she went to Afterlife's VIP room to meet an asari there (reading and paying attention to all of the entries will give you hints as to Morinth's interests when you talk to her later). Following this, you will travel with Samara to the back entrance of Afterlife. She then tells you the only way to draw Morinth out is for you to lure her into taking you back to her apartment. Proceed into Afterlife.

 Note: It is highly recommended that you save at this point. It is extremely easy to fail the first time around, and you will have forfeited the quest, along with the chance for Samara's loyalty.

You must now gain Morinth's attention. This area isn't too big; it is just a small semicircle with a few lounges, a bar, and a dance floor. It is recommended to have a high paragon or renegade skill, however it is not required.
 * Talk to the NPC on the immediate left about concert tickets (this unlocks a conversation option for the next part).
 * Go to the bartender and convince him to serve a round of drinks on the house.
 * Dance with someone on the dance floor.
 * Talk to the two turians (ends in you beating them).
 * Talk to the man who is worried about his sister, an undercover reporter. Then talk to the sister and use the dialogue options in the correct order to alert the sister.
 * Insult the krogan. If Shepard has enough Renegade points, an option to 'step outside' is available immediately. Otherwise, keep choosing the bottom choice. In the end, the krogan backs off, muttering.

After two or three actions, Morinth approaches you and invites you to her private booth. This is the trickiest part of the quest; if you read all of Nef's journal entries (or examined the sculpture on her desk) the correct options become available. You must choose the conversation options that "interest her" or she will simply lose interest and just buy you a drink.

Samara mentions what topics she is interested in if you decide to talk to her before you enter the cutscene. There are five subject choices you can choose from. Don't choose the ones about family or the Justicar, as they will end the conversation quickly. The other three will bring you into conversations about those topics. Choose art and then the artist that sculpted the piece on the last victim's desk (you'll recognize the name). Choose music and use the band from the conversation at the entrance. Choose travel and say you go around the galaxy a lot, exploring the unknown. When power comes into question, use the lower, more aggresive topic. Generally, it is best to be as dark and mysterious as possible, instead of heroic and mighty, as it coincides with her nature. It may take you a few tries, but if you are successful on all three subjects, she will invite you back to her apartment.

Spend some time examining all her stuff before you talk to her. Make sure to scan the Assault Rifle under the sword for a damage bonus upgrade. If you do not have a full Paragon or Renegade score, or did not choose those options in the conversation, Samara will eventually burst through the door and a fight will ensue. After she defeats Morinth she will become loyal to you and gain access to the Reave skill.

If you choose only the Paragon or Renegade options throughout the conversation (this requires an almost completely filled Paragon or Renegade score), Samara and Morinth will become locked in a stalemate and you will be able to choose whether to kill Morinth or Samara. Morinth will be automatically loyal to you should you decide to obtain her, and her fourth skill is Dominate, an extremely useful skill for the last mission. Choosing Morinth will net you a sizable amount of Renegade points. Samara, however, is more powerful overall with better biotic damage and skills, and carries the powerful Reave skill. Deciding on Samara will net you Paragon points. Regardless of the outcome, you will have the loyalty of your chosen asari and are one step closer to challenging the Collectors.

 Note:  You can still gain the Reave power yourself with advanced training even if you choose Morinth.

Tali: Treason
When Tali is accused of treason by the Migrant Fleet's Admiralty Board, Shepard and team has to travel there to attempt to clear her name. She is put under treason for allegedly sending "live" geth parts back to the Migrant Fleet and compromising the security of one of its science ships. Shepard has to attempt to take back that ship to clear her name. In the mean time, they find evidence that clears Tali's name, but points to the recklessness of Tali's father and his team, which may have caused the incident. Shepard has the option of turning in the evidence, or withholding it during the trial. Certain choices have different consequences. These are:
 * Should Shepard decide to present the evidence, Tali is exonerated, but she considers this a betrayal as she pleaded with you beforehand to not tell the Admiralty Board about it. This does not secure her loyalty.
 * Withholding the evidence will result in Tali being exiled, but as she is thankful that her father's legacy and honor are protected, you gain her loyalty.
 * Through certain Paragon choices (if available), Shepard can reference Tali's valor and heroism from events in Mass Effect (e.g., the battle of the Citadel, stopping Saren/Geth/Reapers, etc.), thus swaying the Admiralty boards opinion and leading to her exoneration. This results in keeping Tali's father's honor intact and exonerating Tali from the accusations, successfully securing her loyalty and causing her to fully accept her new name of Tali'Zorah vas Normandy. Choice rewards plenty of paragon points. Choosing the Renegade option will have Shepard yell at the admirals, accusing them of making the trial into a show for political factions advocating peace or war with the geth. They see the light and exonerate Tali. After this, Tali says nobody yelled at the admirals in a long time.
 * Another choice is possible should Kal'Reegar and Veetor be alive and present in the trial. Shepard can appeal to the crowd, resulting in Kal'Reegar and Veetor vouching for Tali, saying that if she is exiled, they are as well. The Admiralty Board capitulates and exonerates Tali. This choice also secures Tali's loyalty. This option is only unlocked by talking to Kal'Reegar, Veetor, and each Admiral prior to departing for the captured ship.

At the end of the trial, Shepard is allowed some final words regarding the Migrant Fleet's stance against the geth. You can choose to ask them to not attack the geth and save their ships for the Reapers, encourage them to find another planet to establish a colony on, or you can wish them luck in their war against the geth. This may or may not have an effect in Mass Effect 3. Choosing the Paragon option on Tali's behalf and selecting the "Don't Go to war" grants a massive amount of Paragon points (+34). This is more than requesting Mordin to not destroy the genophage workings.

For additional dialogue, first acquire Legion, and then bring him on board the Migrant Fleet ship along with Tali. You will have to convince the quarian guards to let him onto the ship, otherwise he will be forced to return to the Normandy. (Note that this option grants the opportunity to gain several Paragon/Renegade points, which can be handy for maxing out those scores to unlock the most options in the Jack and Samara loyalty missions).

Thane: Sins of the Father
Thane will ask that you help him find and stop his son on the Citadel, who has followed in his father's footsteps and become an assassin, and to make amends. Travel to the Citadel and choose Thane as one of your party members. Go and talk to Captain Bailey in the C-Sec office and select the option to discuss Thane's son. He will say that Thane's son was spotted talking to Mouse, a street urchin. You can find Mouse outside the Dark Star club. Talk to him and he will say that the son's target is a local anti-human politician. Go back to Bailey and have him bring in a local crime boss, in order for you to ask him a few questions. After a rather amusing episode of you and Thane interrogating the crime boss by playing "good cop/bad cop", you will be placed on catwalks running the length of the route.

Before doing anything else, pick up the datapad for a Heavy Pistol damage upgrade. Follow the politician (easily visible due to his bright red krogan bodyguard) and, each time there is a box to update Thane, activate it. Near the end of the route you will bump into a stock boy; use the Renegade interrupt to knock him out or talk him down using a dialogue option. After this, you will arrive at the politician's apartment, as the son attempts the assassination. Choose the Paragon option to have Thane and his son have a nice long talk. That is the end of Thane's Loyalty mission. Thane's loyalty mission is one of two which requires no combat (the other is Samara's mission).

 Note: While you are on the catwalks, failure to update Thane each time before the timer bar runs out will result in Thane's son successfully murdering the politician, mission failure and not receiving Thane's loyalty.

Zaeed: The Price of Revenge
Zaeed must travel to Zorya and complete an earlier assignment before he can turn his attention fully to Shepard's mission.

Move through the forested areas and dispatch the enemies guarding the checkpoint. Enemies in this mission consist mostly of various types of Blue Suns soldiers (including Heavies, armed with missile launchers, and Pyros, armed with flamethrowers). After the fight there will be a cutscene at the bridge, where Zaeed explains his prior history with the Blue Suns. Continue to the gatehouse, where Zaeed will confront Vido Santiago and begin shooting at the refinery's gas pipes. Kill the enemies and open the door.

At this point, Shepard must choose either to put out the fire thus saving the lives of the refinery workers or to pursue Santiago and leave the workers to burn to death: At that point, both paths will lead to a hallway where Shepard can pick up the M-451 Firestorm flamethrower heavy weapon. There will be two enemies and a weapons locker with power cells right beside it.
 * Save the workers (Paragon) - This path provides Shepard with two salvage options (each worth 6000 credits) and the Heavy Ammo Upgrade. Use the fuel valves to clear a path to the control room, and activate the fire suppression system.
 * Pursue Vido (Renegade) - This path provides a salvage option (worth 6000 credits) to the right side of the room after killing a group of five enemies. Proceed down the passageway to obtain the Assault Rifle Damage upgrade from the research terminal and then battle a group of nine enemies. Near the end of the path, Shepard can pick up a crate of palladium.

After entering the large room, waves of Blue Suns mercenary enemies (including Pyros) will arrive to fight the player and delay Shepard's squad. Take them out; watch out for the Pyro enemies and do not allow them to close into range. The tanks on the ceiling can also be shot to cause them to fall onto enemies standing below. The final wave consists of a YMIR Mech. After clearing the room, check the small rooms to the side for salvage, and the proceed out the large door.

What happens next depends on the choice the player made earlier during the mission. If the player chose to assist Zaeed, he will kill Santiago and the mission will be over, with Zaeed's loyalty secured. If Shepard chose to save the workers, Santiago will escape in his Gunship. A Paragon dialogue option allows Shepard to make Zaeed loyal, otherwise Zaeed's loyalty will not be secured.

Suicide Mission
Before starting the Suicide Mission purchase the armor, weapon, and shielding upgrades for the Normandy, as for each one of these not purchased a squad member will die during the run to the Collector base.

There are three stages to this mission, during which you will have to choose members of your team to perform certain duties. Picking an inappropriate character for those tasks will result in someone's permanent death. Appropriate choice are listed after Ideal, while inappropriate choices are listed after Non-Ideal.

 Note:  If an ideal squad member is not loyal for your playthrough, consider them to be a non-ideal choice.

If at the end of the final battle all squad members have died, no one will help Shepard onto the ship, resulting in the Commander's death.

Collector Base: Infiltration

 * A Specialist Technician is required to infiltrate via the station's vents to bypass the defenses and doors and open the central gate for the rest of the squad.
 * Ideal: Tali or Legion
 * Non-Ideal: Anyone else, as they will be shot in the face while forcing the door shut. However, if a disloyal Tali or disloyal Legion is selected, the technician will still die.
 * A Fire-team Leader is required for the second team. The briefing conversation mentions that this member must be experienced in leading a team.
 * Ideal: Garrus, Jacob, or Miranda
 * Non-Ideal: Anyone else, as they will get your specialist technician killed, even if Tali or Legion was chosen.
 * Your Team – will be fighting against Collector Drones, Harbingers, and several Collector Assassins, which all have biotic barriers on harder difficulties (Drones gain barriers on Hardcore and Insanity only). Characters with Warp or Incinerate powers are a good choice, as Warp is effective at taking down biotic barriers and armor, and Incinerate deals decent damage against organic enemies along with setting them on fire for a few seconds, and it does some damage against barriers.

You will have to fight several Collector squads, while pressing forward to activate 8 different consoles alongside a path beside the vent your Specialist is in. The heat in the tunnel will kill your specialist if you take too long getting to the consoles, so you should clear out the enemies as quickly as possible. Another tactic (although it can take a few tries depending of how skilled you are and the difficulty level) is to ignore enemies and simply rush ahead opening all the consoles in your way. It is advisable to save your game before you press the last button in case you pick the wrong character for the next session. The mission immediately ends after pressing the final button, so if time is running out it may be worth it to run to the button and press it even if there are enemies remaining.

Collector Base: The Long Walk

 * A Biotic Specialist to generate a shield, protecting the squad against Collector swarms.
 * Ideal: Samara/Morinth or Jack.
 * Non-Ideal: Anyone else. Doing so will result in one of your squad mates being carried off by a Collector swarm.
 * A Fire-team Leader for the second team.
 * Ideal: Garrus, Jacob, or Miranda
 * Non-Ideal: Anyone else. There is a possibility of this leader dying as the doors close at the end of the long walk (shot in the stomach as the door closes). (Also, Miranda will not die here even if disloyal.)
 * An Escort to guide the Normandy crew back to the ship. However, you can't use this person for the final battle. Choosing no one results in the death of the Normandy crew.
 * Ideal: Mordin. This will ensure his survival because he has a strong chance of dying if he doesn't escort the crew back, even if he is loyal. An explanation is given here. Otherwise, any loyal squad member is guaranteed to successfully escort the crew back to the ship.
 * Non-Ideal: A team member that you have not secured loyalty from. This squad member will perish while escorting the Normandy crew, sometimes the crew as well.


 * Your Team – You will be fighting against Drones, Harbinger, Assassins, waves of Husks and Abominations, and one Scion.

The Biotic Specialist you have chosen will erect a dome-shaped biotic shield encapsulating the squad from Collector swarms. Note: moving outside of the biotic barrier will cause damage to Shepard and eventually result in death. The Biotic Specialist will move slowly through the level and stop three times for you to fight off a wave of enemies before proceeding. The waves encountered are:
 * 1) Drones and Harbinger
 * 2) Husks and Abominations climb up from a ledge then Drones, a Harbinger and Assassins will appear.
 * 3) Husks, Abominations, and a Scion.

Final Battle
Note that, while manual saving is not allowed from this point onwards, the game will auto-save at the beginning of each part. Loading an auto-save also gives you the opportunity to change the weapons loadout of your squad. If you die, you will have full ammo when you reload the game, even if you didn't have full ammo at the last save.

Part 1 – Team Selection

 * The team you pick here will stay with you for the rest of the suicide mission – you will be fighting against Drones, Harbinger, Assassins, Abominations, Scions, and one giant Human-Reaper larva.
 * Ideal: Squad members that are loyal to you and are less suited for defensive tasks such as Mordin, Jack, Legion and Tali.
 * Non-Ideal: Squad members that are not loyal to you. They will die after the battle as the Collector station begins to fall apart.
 *  Note:  The teammates you do not pick are assigned to hold the line from the Collectors. A 'defensive skill' value is calculated for the 'hold the line' group as a whole, based on a defensive value inherent to each character. Loyal characters gain a bonus to this value. If the 'defensive skill' check is not high enough to ensure all characters' survival, squad members will be designated to die based on their vulnerability, with Mordin taking priority if he is present. Leaving behind strong defenders, such as Grunt, Garrus and Zaeed will increase the group's odds of survival. In contrast, certain characters such as Jack, Tali and especially Mordin have less skill in holding their position and should be removed through escort duty or taken along. The entire group will survive as long as the combined defensive skill is high enough, otherwise the game picks a squad member to die based on the scenario of who was left behind and how loyal the group members are. (Squad members who are not loyal are most likely to survive here then anywhere else, provided the group's collective defense skill is high enough.)

Ammo is very scarce, so powers must be used efficiently, and ammo must be scavenged when possible. Similar to a previous encounter on the Collector ship, Platforms will fly in, carrying several Collector enemies on them. The last platform will contain three Abominations and two Scions. After defeating them there will be a console to trigger the next section.

 Note:  On both the PC and Xbox 360 versions there is a glitch where the two Scions will not attack until you run up to the platform to engage them. If you have a sniper rifle or Warp you can kill them from 2 platforms away before they are aware you exist.

Part 2 – Destroying the Feeding Tubes
More fly-in platforms with various types of Collectors. After clearing each platform, the armor covering the four tubes of the inactive Human-Reaper will open for a short period of time and you should destroy them immediately (if you're lucky, you can destroy two each round, but this is difficult as their armor covers them very quickly after destroying one. A good tip here is to switch to the SMG or assault-rifle type weapon before killing the final Collector, aiming at the tubes (right-mouse on PC), firing as soon as the shutters begin moving, and switching to the other tube as soon as the tube appears to shatter. Also, if you have heightened adrenaline rush it is possible to take out all 4 in one round. A good weapon to use is the X-6e Carnifex Hand Cannon, if you have either version of Adrenaline Rush and are fast enough, the Carnifex can destroy each tube in one shot, thus allowing you to finish in one round). You can take out two tubes with the M-15 Vindicator if you shoot quickly enough, even without Adrenaline Rush. If you have the M-920 Cain or the Collector Particle Beam, it is also possible to take out two tubes simultaneously, although you may want to save your ammo for the final battle. It is also possible to destroy the tubes or at least heavily damage them by using warp, so having squad members with this ability can be useful.

Destroying the four tubes will cause the Reaper to fall into the chasm below. Shepard will open up the platform's core and prepare to plant a bomb, but will be contacted by the Illusive Man, who asks if you will destroy the facility (Paragon), while preferring that you keep the facility for Cerberus to use against the Reapers (Renegade).

Part 3 – The Human-Reaper Larva
You start behind a good barricade spot and you can start shooting at the Reaper's eyes (they are small, but there are 3 of them, one in the right socket, two in the left), or the large weak point on its chest. It has a nasty charge up attack and it would be wise to not expose yourself until it is done. If you are hit by it, your shield will be depleted and will take longer than usual to recharge. (If you're feeling brave, you can also take advantage of the fact that it stays still while charging its attack to get in some reliable damage; listening to the charge-up sound will tell you when it's time to get back behind cover.) Be aware that the Reaper's glowing mouth is vulnerable to your weapons while this attack is charging, and presents a very large target for gunfire. Note that you can fall off the platform you are on, so stay away from the edges.

Once you have damaged the Reaper enough, Collector drones will attack. During this section of the fight Harbinger will drop special Heavy Weapon ammo packs when killed. Also note that the Reaper's mouth weapon will injure or kill any Collector enemies it hits. When the boss' life is below 25%, it will begin dodging around and send more attacks at you. Continue shooting at its eyes or use the M-920 Cain, directed at its chest and the fight should be over shortly, leading to the end of game cutscenes. Sniper rifles are surprisingly effective: when the Reaper leans to the right there are about 3-5 seconds worth of reliable targeting. After the first shot, an Adrenaline Rush (if available) allows for a second reliable shot. This has the advantage of spending very little time outside of cover (just enought to fire two shots), allowing for little to no damage to Shepard.

Epilogue
The Normandy rushes to escape the immense fireball emanating from the Collector base. If Shepard chose to destroy the base, it explodes in a massive blast that the Normandy barely manages to outrun. If the base was spared, the blast is blue as the radiation destroys all organic matter, leaving the base intact. After the mission ends, there are three possible endings:
 * Shepard goes to speak with the Illusive Man. If the base was destroyed, the star behind the Illusive Man now appears to be blue. The Illusive Man is furious with Shepard; he tells the Commander that they still have to face the Reapers and that base's technology could have helped them.
 * If the base was spared, the Illusive Man compliments Shepard's decision. When their discussion is finished, the Illusive Man sits in front of the star, contemplating a hologram of the spared base.
 * If your actions caused Shepard's death in the final cutscene, Joker is the one to speak with the Illusive Man.

In dark space, a Reaper is shown awakening from hibernation as lights appear within its superstructure. As it awakens, the dark void surrounding the Reaper is illuminated by thousands of pinpoints of light, revealing hundreds, or even thousands, of other Reapers. The final shot shows the Reaper fleet with the Milky Way galaxy in the distance.

After completion of the last mission, cutscenes and closing credits you will have the option to either: a) Go back and complete any missed side or loyalty missions, planet scans, free-roam, etc, or b) start a new career using the same "Shepard" with your stats carried over.

 Note:  Starting a new game + will carry your character's stats over, but not your Paragon/Renegade scores. Your bars will be completely empty, even if you had a previous bonus from carrying over your character from Mass Effect.