Mass Effect 2 Guide

This page contains a full walkthrough for the main missions of Mass Effect 2.

Note: Changes from Mass Effect
There are a few main differences from Mass Effect that returning players should pay attention to. Most of them are introduced in the initial mission, which serves as a tutorial.
 * The Powers/Tech system has been significantly overhauled. Using a Power/Tech now trips a cooldown on all other Powers/Tech as well as the cooldown on the one the Player used. However, to compensate, the cooldown on Powers/Tech has been significantly lowered, from between 120 - 45 seconds to now between 9 - 3 seconds. Shepard's cooldowns on his Powers/Tech are often much shorter than the same power on an NPC ally.
 * You do not automatically go into cover by moving up against an object. To get into cover, you have to get next to an appropriate object and then press [Space] on the PC or (A) on the 360 to get into cover. If you are sprinting towards an object you can take cover behind you will instantly do so when you reach it.
 * Instead of simply climbing on top of low cover, you are now able to simply flip over it if it is small enough with [Space] or (A).
 * Gunfire has changed dramatically. The guns now behave more like real life firearms. This means if you are trying to hit a moving target you need to lead your target. Damage calculations are no longer dependent on skills or levels.


 * Weapons now have an ammunition mechanic, in the form of ejectable heatsinks. All small arms use the same types of heatsinks; heavy weapons utilize power cells. The overheating mechanic in the first game has been removed; certain tech skills can still briefly disable weapons.
 * Most interactions are now done with [Space] rather than [E] on the PC but operate the same on the console.
 * The leveling system has been significantly overhauled, resulting in characters having from 4 to 6 skills to level instead of 15-20. Each skill has 4 levels, with the fourth evolving the skill in one of two ways, usually either strengthening the skill, or causing it to have an area effect, although each is different.
 * The game has done away with weapon skills, making all weapons 100% effective at the start of the game. This has a significant effect on weapons like sniper rifles, which no longer have scope bob.
 * Tech and Biotic powers can now arc over cover to hit their targets, no longer requiring direct line of sight to use them. They can however still miss.
 * Instead of Intimidate and Charm skills, your ability to pick persuasive options in dialogue is determined directly by your Paragon or Renegade score.
 * In addition to Paragon and Renegade dialogue choices, there are also Paragon and Renegade interrupt options. These are signified by a flashing red or blue icon during a cutscene; press the appropriate mouse button or trigger to engage in the interrupt. There is usually a limited window of time during which the interrupt can be triggered. Interrupts do not have Paragon or Renegade score prerequisites, but award large numbers of Paragon or Renegade points.
 * Upgrades are now permanent rather than interchangable. However, the method of obtaining upgrades has changed. Rather than simply purchasing upgrades or finding them on corpses, you now must now find the upgrade blueprints on missions, ask your teammates about potential upgrades, or purchase upgrades in stores. Once you have Mordin on your team, you can go to his research lab and create the upgrades using resources that you find on missions and while scanning planets. Upgrades purchased in stores do not have to be 'built' in the lab.

Save Joker
The SSV Normandy SR-1 is under attack from an unknown enemy (later revealed to have beeen the Collectors). 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, and awaking to station alarms, walk to the locker to obtain a pistol and armor. Miranda Lawson will introduce herself over the radio and give Shepard instructions.

Use the cover command to avoid damage from the explosive, then continue on through the open door and over the next obstacle.

Take cover in the next room 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, (it might be a good idea to knock them down and kill them for the Brawler achievement), and needless to say, Overload and AI Hacking would make this part a lot easier for you, if you are on a harder difficulty.

There will be recordings by Miranda and Dr. Wilson about their experience reviving Shepard, and an intro to the hacking and routing mini-games, but nothing else of much note.

Eventually you will meet Jacob. After clearing the room with Jacob and a little bit more dialog, Shepard and Jacob will meet up with Miranda's assistant, Wilson, who you will have to heal using medigel and your unity power. After some dialog you will head forth toward the shuttle bay and face a few more enemies. In the bay where the second wave of mechs attack, you will find a datapad which you can then attempt to hack (if you fail, you can retry as many times as you want until you get the hang of it). The mission ends when you arrive at the shuttle bay and meet with Miranda.

Freedom's Progress
Upon arriving at the colony, proceed through the door and make your way through the colony, killing any LOKI 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 meet and confront Tali and a group of quarians. After talking to Tali, continue through the door - note the combat drones which fly past your squad. Enter the next area through the gates. Here, the combat drones (a 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's rockets.

Continue to move forward. Eventually, Tali will contact you saying that the other quarians moved on in an attempt to steal the objective. 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 equipped with a rocket launcher and machine gun. Do not expose yourself - its weapons can incapacitate you within moments. Also, move from one piece of cover to the next. The YMIR advances on your position and may flank you if caught off guard. Once destroyed, scan the mech for a heavy weapons upgrade, and check the buildings on either side for items/creds.

Finish the mission by entering the building your objective marker points to, where a delusional quarian watches a bank of screens. Paragon/Renegade Interrupts are presented to you in your communication efforts with this quarian. Tali walks in shortly afterwards. 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 mission will end with your final decision.

Normandy Crash Site (Optional)
If you downloaded the Normandy Crash site mission you will receive a request from Alliance Command that you erect a monument at the Normandy crash site and collect the dog tags of fallen crew members to return to their families. There is no combat on this mission, however there are various Mass Effect 1 "flash backs" that Shepard will encounter as well as random "goodies" (thermal clips, resources, etc.).

The Professor
It is advisable that the player recruit Mordin first because it allows the player to upgrade their equipment, which can then be used on all subsequent missions. Head to Omega, and then talk to the turian guard who is responsible for enforcing the quarantine. 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. Bypassing locked doors will allow you into apartments, some of which contain refined resources. 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. 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.

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 throught the hallways, check for footlockers containing cash and raw materials. In addition, you will be given the oppertunity to disable/sabotage the mech and/or dropship. When talking to the dropship's mechanic, a renegade interrupt will flash. Doing so will cause you to "remove" the mechanic and halt the dropship's repair. 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 disscussion over events to occur, the mercenaries begin their assault. Shepard and his team have to defend Garrus and his position from waves of mercs, including a massive battle walker (the mech you did or did not sabotage). After a few waves are cut down, the mercenaries begin drilling their way through the sealed passageways below. Shepard takes his team below ground to reach 3 sets of blast doors in order to lock them off for good. After a long firefight, Shepard makes his way back up stairs were the mercs 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. iI 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. (provided and tested by Xbox360 GT: RKO x Cold Ice.)

After defeating Gram, the fighting stops, and Garrus reccomends making a break for it across the bridge. Just as you are about to leave, a dropship appears and guns down Garrus. Winning the fight is tough, but with enough engineering and biotic abilites, 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 had been 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.

The Convict
The Convict Aka Jack 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 to line his pocket book and quickly attempts to capture Shepard and sell him/her to a client. After fighting your way out, Shepard releases Jack, who proceeds to start destroying the Purgatory. Following her, you eventually find the Warden, who has shielded himself with a number of shield generators. After destroying the generators and killing the Warden, Shepard tracks down Jack and convinces her to join him.

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 Sun troopers, enemies count at 3. After that, go on and you will have to talk to the Wounded Merc, after getting information on The Warlord continue down the road. Enemies will be waiting for your on top of the ship deck. 2 on the front port, 2 on the bridge and 2 on the far bridge. Do not forget to get the 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 3.

Continue down, there will be a Tank-Grown Krogan to talk to, before being able to talk to him, there will be 5 more enemies to kill, easy ones. 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 2 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 an update! (adds more damage to your squads sniper)

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, you will met with a old friend from Virmire, her name is Rana Thanoptis.(she will only be there if you imported 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 lad terminal (updates Krogan Vitality by 25%).

Now the fun kicks in, there will be a boss fight, Jedore, and her “army” of krogans and an few YMIR Mechs.


 * Important** 3 Headshots should kill Jedore if you are a Soldier or an Infiltrator in normal difficult. In Hardcore difficulty, 4 headshots is required with the upgraded bolt action rifle (2nd playerthrough). Killing Jedore will stop the any remaining krograns from being released to fight you.

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.

Over the Horizon
A short cutscene shows Ashley Williams and other Alliance soldiers speaking and working with colonists, followed by a strange ship (revealed to be the Collectors) attacking the entire colony in order to abduct them. Upon arriving with your party, you will have your first encounter in the game with the Collectors. Ignore the "frozen" humans (you can't interact with them) and fight your way to the end of the map. Take constant cover in the large cargo area that's infested with Husks, an Abomination and a Scion, in order to activate the large cannons to drive the Collectors ship away, thus sparking a rather interesting conversation with Ashley.

Upgrading the Normandy
Before reaching the end of this section of the game, you may want to upgrade your ship. Upgrading your ship will save some of your crew members. The important upgrades are the shields, the armor , and the cannon. Jacob, Tali, and Garrus 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 upgrades early.


 * Shields: Tali/Legion/other; I don't know what happens if they are both in your current squad to take down the oculus. They/she are/is vaporized when the drive core explodes due to stress.
 * Cannon: Thane/Legion/Garrus/Other; You lose a party member when the Collector ship attacks you. If Tali and Legion are in your squad fighting the occulus - Garrus will die.
 * Armor: Jack/Unknown; You lose a party member when you crash.

Hypothetical, but the loss of squad member may be randomly chosen.

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
TODO

Tali
TODO

Collector Ship
After recruiting two of those crew members, you must board a disabled Collector ship. This will happen after the Illusive Man 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 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 being operated and experimented on. Another conversation between squadmates 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 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, such as shotguns for infiltrators. 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 shotgun M-300 Claymore Heavy Shotgun, the light machine gun M-76 Revenant, or the sniper rifle Widow Anti-Material Rifle. The weapon chosen must have the basic training associated with its class, ie. the M-76 Revenant requires the ability to use assault rifles, thus only useable by soldiers. It is not possible to have all three for Shepard, despite multiple playthroughs.

After proceeding further, you will lose contact with the Normandy and need to reach a platform to reestablish communication with EDI. It will come to light that the entire mission was a booby trap staged by the Collectors to trap the Normandy (which the Illusive Man was quite aware of). Shepard et al will have to fight their way back to the shuttle and afterwards you can have your choice of words with Illusive Man for sending you into a trap.

Reaper IFF
This mission will pit you against husks, abominations and a few Scions. If you find yourself walking toward a group of explosives, it is probably an ambush site where mobs of husks and abominations will rush you from the edge of the platform. There are several weapon upgrades sidelined throughout this level so remember to search. Halfway through the mission, Joker will call and inform you that the Reaper threw up shields. You will then be tasked with destroying the mass effect core of the Reaper. As you are advancing toward the core, a cutscene will trigger showing a single geth soldier with N7 armor kill a few husks around you. The player will then fight until 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. Missiles are strangly misdirected by the core and firing one will result in the missile flying to the left or right. After destroying the core, the player will be given the choice of bringing the geth back to the Normandy. If you choose to do so, the geth may be recruited and become known as Legion.

Activating the IFF
It's important to complete all loyalty missions and upgrades before this point.

The IFF will be integrated into the Normandy in order to use the Omega 4 relay. In order to do this, they will have to perform a test on the system. Joker will inform you that the crew should use the shuttle for the next mission. (I think I ignored that and did other missions first, but I'm not sure.) If you agree, all of your crew members board the shuttle, leaving Joker and the Normandy alone.

Joker must put EDI in control of the ship, which involves you playing as Joker and hobbling to the Tech Lab (follow the lights on the floor), and then to the AI Core in the Medical Lab. 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 in, one will spot you, and the mission will end. Instead, move to the stairs and wait until EDI tells you that the corridor is clear.

When the core is restarted, Joker is the only one on board. Shepard has a decision to make: either head straight to the Omega 4 relay, or complete more loyalty (or side) missions. If you don't go immediately through the relay (you can still do research first), Kelly Chambers will die on the Collector ship. If you go through the relay immediately, Lilith (a colonist from Horizon) will die instead. Either way, you get a gory cutscene.

Interlude
These missions are optional but can affect the final outcome of the game.

Note on Loyalty Missions
Each character you can acquire for your party has a corresponding 'loyalty mission'. Completing this mission successfully is required to gain the party member's loyalty, and unlocks the party member's fourth power and an alternative costume.

Loyalty missions become available as the game is played. Yeoman Kelly 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.

Confrontation Interludes
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 afflicted character is permanently compromised.

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 loyality. 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.

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.

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.

Jacob: The Gift of Greatness
Jacob recieves a message he believes was sent by the Illusive Man that informs him that a distress beacon from Jacob's father's ship has been discovered after 8 years. You quickly leave for the planet and discover the wreckage of the ship and the V.I. After talking with the V.I. and exploring the ship, you come to discover some rather disturbing facts. After the ship had crashed, Jacob's father was promoted to captain as the captain had died during the crash. Shortly after landing on the planet, they discovered that the plant life affected their brains, making them stupid and in the case of the men, violent. You also find out that Jacob's father had forced the crew to eat the plants on the planet, while the officers used the supplies of the ship. Jacobs father also divided up the women among the officers. After fighting your way through the crazed crew and the robots, you find Jacobs father, who is at first relieved to be rescued until he realizes that his rescuer is his son. After berating his father, you have the option of either subduing him and leaving him for the Alliance to pick up and prosecute, leaving him stranded on the planet in to deal with the mess he has created as his punishment, or giving him a pistol, which he will use to kill himself after you leave.

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 recieves 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 ME1. 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. During the meeting, you can either help Garrus and facilitate Sidonis's assassination, or inform Sidonis and spare his life.

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 kogan and mercs until you find Mordin's old associate, who has not been kidnapped, but is instead working on a genophage cure, riddled with guilt. 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.

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 Jack's the truth about her childhood was a little different than she remembered. 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.

Thane: Sins of the Father
For Thane's loyalty mission, he will ask that you help him find his son on the Citadel, who has followed in his fathers footsteps and become a assassin, and make amends. Travel to the Citadel and choose Thane for your party. Go and talk to Captain Bailey in the C-Sec office and select Thane's son option. He will say that his son was spotted talking to Mouse, a street urchin. You can find Mouse outside the Darkstar club. Talk to him and he will say that the son's target is a local anti-human politician. After a very awesome cut-scene you will be placed on catwalks running the length of the route. Follow the politician easily seen by his bright red Krogan bodygaurd and, each time there is a box to update Thane, activate it. After this, you will arrive at the politicians 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 Thanes Loyalty mission. Thane's loyalty mission is interesting because it requires no combat.

Note: Failure to maintain visibility on the politician (thus updating Thane on his whereabouts) while you are on the catwalks will result in Thane's son succesfully murdering the politician, mission failure and not receiving Thane's loyalty unless you reload from a previous save point.

Grunt: Rite of Passage
Bring Grunt before the Krogan clan leader in Tuchanka, if you kept Wrex alive in Mass Effect 1, he will be the clan leader. Grunt will be instructed to take a series of tests before a structure called the Keystone. The Keystone will send out 3 shockwaves, one at a time in varying strength. The first shockwave brings waves of varren, standard melee units. Second shockwave brings some kind of firebug that explodes when shot. Third wave brings a thresher maw that 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 3 minute timer with the sole objective of suriving. THe second option is to to kill the thresher maw within the 3 minutes. Not a particularly daunting task, but you will unlock an achievement if you do. Killing the worm will trigger a scene involving another clan of Krogan attempting to recruit Grunt. A fight will ensue against a group of 6 or so Krogan. Killing them will result in the end of the mission.

Samara: The Ardat-Yakshi
When you get the quest,you have to go to Omega and and check on one of Mornith's latest victims, a female Human named Nef. Head to the appartments to find Nef's grieving mother. After a short conversation with her, you are allowed to search her appartment for evidence. Read her holograph journal's last entry to discover that she went to the 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 interests when you talk to her later). The final words were that she was supposed to meet her the next day. Following this, you will travel with Samara to the back entrance of afterlife. She then tells you the only way to draw her out is for you to lure her into taking you back to her apartment. Proceed into Afterlife. (Very important... 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 reccommended to have a high paragon or renagade skill, however it is not required. Talk to the NPC on the immediete left about concert tickets (conversation hing), go to the bartender and tell him to order a round of drinks, then go and dance with someone on the dance floor. It really doesn't matter what you do but you must do some useless tasks in order to draw her attention. After two or three things are done, you will instantly go into a cutscene where 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 this is relatively easy. 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. 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. After engaging in converstation, Samara will burst through the door and a fight will ensue. Eventually the fight will become locked in a stalemate, and you will have to choose whether to kill Morinth or Samara. Morinth will be 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 sizeable amount of Renegade points. Samara, however, is more powerful overall with better biotic damage and skills, not to mention the Reave skill. Vice versa to Morinth, deciding on Samara will net you Paragon points. Regardless of the outcome, you have the loyalty of your chosen Asari and are one step closer to challenging the Collectors.

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 and his squad team 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 1 (e.g., the battle of the Citadel, stopping Saren/Geth/Reapers, etc.), thus swaying the Admiralty boards opinion and leading to her acquittal. 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.
 * Another choice is possible should Kal'reegar and Vee'tor be alive and present in the trial. Shepard can appeal to the crowd, resulting in Kal'reegar and Veet'tor 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.

At the end of the trial, you are 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.

For additional dialogue, first acquire Legion, and then bring him on board the Migrant Fleet ship along with Tali. You may have to convince the Quarian guards to let him onto the ship, otherwise he will be forced to return to the Normandy.

Legion: A House Divided
After a while, Legion will inform you that geth actually are ambivilant 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 geths. You need to fight your way to the central computer core. Once there, Shepard can decide whether to reprogram the virus and use it to free the heretics from Reaper-control or to destroy it and the space station with all heretics on it. If reprogramming is chosen, Legion will inform Shepard that the heretics will return to the geth and their memories incorporated.

Zaeed: The Price of Revenge (DLC)
You will receive a Mission on Traveling to Zorya. After walking/running thought the forested areas, you will encounter your first enemies, Blue Suns Troopers, pyro, heavy (using the ML-77 Missile launcher) and a Fenris Mech. Using overload on the Pyro will immediately kill him. There will be a Medi-kit around behind cover. After the fight a cut scene come when reaching the bridge. Continuing down to the Gatehouse there will be a crate of Refined Palladium. Again another cut scene will pop up when opening the door. There will be 2 enemies after the cut scene when reaching the cross section, and to the right there will be another crate of Refined Palladium. After, opening the door another cut scene will pop out. The cut scene added 11 Renegade for me.

At this cut scene, the player has a choice to either save the factory workers, who will die in the fire, or to assist Zaeed on his mission of Vengeance.

No more cut scenes from now unil the end. There will be a Salvage(+6000 Credits) to the right side of the room after killing your first 5 enemies, going down the passage way there will be a Research Terminal (gives a updated on your Squad assault rifles’ damage). Going on there will be 9 enemies to kill. Continue on and again there will be a loot on Refined Palladium. Down the hallway there will be a M-451 firestorm(only given by downloading the DLC), which is basically a flamethrower. There will be 2 enemies and a Weapon Locker with power cells right beside.

Now this is where the fun kicks in. Enemies including the YMIR Mech will come after you. After waves of enemies the YMIR Mech will come last. Do not forget the Medi-kit; it is useful! The place where the Blue Sun Troopers spawn, the left and the right have some good stuff for you. (Top Left side doors, Salvage (+6000 Credits). Top Right side doors, Salvage (+6000 Credits)). Continuing on there will be a last cut scene.

The last cut scene will depend on the choice the player made earlier. If the player chose to assist Zaeed, he will kill Santiago and the mission will be over, with Zaeed promoted to "Loyal". If the player chose to save the workers, if he has sufficient paragon points, he will be able to use a charm dialogue option and ensure Zaeed's loyalty. Otherwise, the loyalty mission fails and Zaeed remains "normal".

Suicide Mission
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 permanently dying after the first or second session.

If you have chosen Morinth over Samara in Samara's loyalty quest, the skill Dominate is your best friend in this part because it allows you to control unshielded collectors - if you haven't noticed by now, enemies always target the closest target. On the other hand, AI Hack is no longer useful. The following is the combination needed to avoid anyone dying (provided that the Normandy is properly upgraded and all crew members are loyal).

Collector Base: Infiltration

 * A Specialist Technician is required to infiltrate via the station's vents in order to circumnavigate the defenses and doors, in order to open the central gate for the rest of the squad. (Pick: Tali or Legion. Do not pick: Thane, Jacob, Mordin or Garrus as they will die. Needs confirmation.)
 * A Fireteam Leader is required for the second team. The briefing conversation mentions that this member must be experienced in leading a team. (Pick: Garrus/Miranda/Jacob, Do not pick: anyone else, as they will get your specialist technician killed. Needs confirmation.)
 * Your Team - will be fighting against Collector Drones, Harbingers, and several Collector Assassins, so it is wise to bring along members that wield biotics.

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 last few consoles are time-sensitive, so you should clear out the enemies as quickly as possible. 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. (Pick Samara/Morinth or Jack. Don't pick: Miranda, Thane or Jacob. Doing so will result in the death of one of your squad mates.)
 * Fireteam Leader for the second team. (Pick: Garrus, Miranda, Jacob. Don't pick: Thane, Grunt, Zaeed, Legion, Tali, Mordin, Jack or Samara.)
 * 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. (Pick: Any loyal teammate that was not assigned as a specialist or fireteam leader.)
 * 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: If you have taken all of the necessary precautions no teammates will die.
 * 1) Drones and Harbingers
 * 2) Husks and Abominations climb up from a ledge then Drones, a Harbinger and Assassins will appear.
 * 3) Husk, Abominations and a Scion.

Part 1

 * 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.
 * The rest of the team stays back to hold the line until you're done.
 * (Unconfirmed) If there are two or less characters that hold the line - most likely they never get to the Normandy and will die.

It's the last part of the game thus it makes perfect sense for it to be hard. Ammo is very scarce, so powers must be used efficiently, and ammo must be scavenged when possible. Similar to the encounter on the Collector ship. Platforms will fly in, carrying several enemies on them. The last platform will contain 3 Abominations and 2 Scions on lower difficulty - good luck with it. There will be a console to trigger the next section. You are unable to save, although there are autosave points.

Part 2
More fly-in platforms. After clearing each platform, the armor covering the four tubes of the inactive Human-Reaper will open temporarily 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). If you have the M920 Cain or the Collector Particle Beam, it is possible to take out two tubes simultaneously, although you may want to save your ammo for the final battle. If you are a Soldier, you can use Adrenaline Rush to take out 3 (or if you're fast, all 4) tubes before they close.

Destroying the four tubes will trigger an interlude with Illusive Man, who asks you to destroy the facility (Paragon) or keep the facility for Cerberus (Renegade). If Miranda is in your squad, Illusive Man will order her to destroy the facility. She will refuse if you have gained her loyalty. It is unclear what she does if her loyalty has not been gained.

Part 3
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). It has a nasty charge up attack and it would be wise to not expose yourself until it is done. Once you have damaged the Reaper enough, Collector drones will attack. When the boss' life is below 25%, it will begin dodging around and send more attacks at you (if you are an Infiltrator, your sniper ammo should be your greatest asset at this stage). Keep poking its eyes until it collapses, thus ending the game.

This fight can be ended extremely quickly if you've got good aim and timing. To do this, you'll need the M920 Cain (researched on the Normandy). A successful hit on the Reaper's weak spot (located on its chest) will take a massive chunk out of it, well over 50% of its maximum health. This, combined with sustained assault rifle or heavy pistol fire, will end the battle in under five minutes. Only try this if you have a good aim, however, and dont waste the Cain's ammo before this fight! With the heavy weapons ammunition upgrade maxed out, the Cain can fire two shots; if both shots connect the battle is finished. If the player has the Widowmaker sniper rifle and some type of anti-armor ammo, it does very good damage against the Reaper. An excellent weapon to use is the Revenant Machine Gun with anti-armor, warp, or incendiary ammo equiped; simply spray rounds into the weak spots and the battle will end quickly.

Epilogue
The Normandy rushes to escape the immense fireball emanating from the Collector base. If Shepard chose to destroy the station, the fireball is orange. If the station was spared, the radiation blast is blue. These colors are opposite from the normal Paragon/Renegade colors.

After the mission ends, Shepard goes to speak with the Illusive Man. If the station was destroyed, he is furious with Shepard, who tells him that the threat is still the Reapers. If the station was spared, Illusive man compliments Shepard. The difference also affects the color of the sun behind Illusive Man. If Shepard has not destroyed the station, the sun remains the same red-orange color (renegade) that it has been throughout the game. However, if Shepard destroyed the station, the star is now a blue color (paragon). Illusive Man sits in front of it, contemplating a hologram of the spared station.

Before suicide mission
Necessary - don't do any upgrades to your ship. As many team members as possible should not be loyalty to you.

Optional - complete a few character loyalty quests, but with a negative outcome. For example: expose Tali's father at the trial, and the let the Ardat Yakshi go away in Samara's quest. You can complete a few quests as normal though (for example: for Jacob and Grunt, you still can have a bad ending and those characters will be loyal to you regardless). It is necessary to complete a few quests though (two or three - need a check), because the mission on the collector's ship won't start until after all of your teammates are recruited. You could also do sidequests on the planets instead.

Optional - after your team is kidnapped by the collectors, don't run directly to the Omega 4 Relay. Do as many sidequests as you can (how many- need a check), that way all of the crew, except for Dr. Chakwas, will be dead when you arrive for the suicide mission. You will get different videos with the horrible death of Kelly Chambers and a shocked Dr. Chakwas.

Suicide mission
If there are no upgrades to the ship, 3 of your teammates will die at the beginning of the suicide mission. Most likely it will be Jack, Thane and Legion (If you take Legion with you to fight the Occulus - Tali will die. If You take Thane - Garrus will die).

Collector Base: Infiltration
1. Send Jacob as a technician. No matter if he is loyal or not - he dies.

2. The captain of second group - Thali, Miranda or Samara (it doesn't matter, if Jacob is a techinician he dies anyway).

3. Your team - anybody.

Collector Base: The Long Walk
1. Biotic specialist - Miranda.

2. Send Mordin with the survivors. If he is not loyal - he dies.

3. The captain of the second group - Zaeed (if you don't have the DLC, pick Grunt instead - even if he is loyal - he dies)

4. Your team - Legion and Samara. Legion will die. If he dies on the ship, take Garrus - he will die, even if he is loyal.

Final Battle
1. Take Miranda and Samara with you. After the fight with the boss, if they are not loyal - they die.

2. Grunt and Tali will die, never making it to the ship. If somebody in that team is loyal to you, most likely they will survive and you won't get the bad ending.

3. There will be no one to give Shepard a hand at the end...