This mission is acquired automatically after the completion of Freedom's Progress.
The Stop the Collectors mission is the main plot mission in Mass Effect 2, which mainly consists of answering requests from the Illusive Man that will lead Commander Shepard's team (which will grow along the way) throughout the Terminus Systems, in an effort to deal, by any possible means, with the uncovered Collector threat.
The Stop the Collectors mission starts right after Shepard has found evidence that the Collectors are the force behind all of the recent abductions of entire human colonies in the Terminus Systems. It only ends when Shepard attempts to deal with their base on the other side of the Omega 4 Relay, whatever the outcome.
Assemble a team (1) Edit
Using the Illusive Man's dossiers, assemble a team of experts to fight the Collectors.
After returning from a field investigation at Freedom's Progress with Miranda and Jacob; Shepard has a meeting with the Illusive Man. During the meeting Shepard learns that the team's findings of evidence incriminating the Collectors as responsible for the mass abductions of human colonies confirms the Illusive Man's pre-existing suspicions. Then Shepard, despite any possible misgivings about working with Cerberus, agrees that Cerberus's effort to oppose this new threat upon the Galaxy appears genuine and is worthy of Shepard's involvement.
The Illusive Man then tells Shepard that he should start by assembling a strong team for their now common effort. He explains that most of Shepard's former team has scattered throughout the galaxy and is either unavailable, unaccounted for or difficult to convince to work with Cerberus.
The Illusive Man then presents Shepard with a list of possible recruits to consider, based upon Cerberus's intelligence (Dossier: Archangel, Dossier: The Convict, Dossier: The Professor, Dossier: The Warlord and, if you have access to their respective DLC, Dossier: The Veteran and Dossier: The Master Thief). Shepard and the Illusive Man also discuss the question of involving the Galactic Council, which is left to Shepard's judgment. The Illusive Man then specifies that Miranda and Jacob will continue to serve under Shepard's command.
When ending the meeting the Illusive Man pleasantly surprises Shepard by providing an initial crew member whom Shepard already knows very well: Joker. Joker then leads Shepard to a second large surprise: their ship, the new Normandy SR-2. This part of the mission ends when you have recruited what is considered a sufficient core team (by completing the first four Dossier missions).
Go to Horizon Edit
Go to the human colony of Horizon and stop the Collector attack.
This part starts right after you have recruited Jack, Garrus, Mordin, and collected the pod containing Grunt. Once triggered, you cannot do any other mission. An urgent message from the Illusive Man explains that Cerberus has received a warning of a possible new Collector attack on Horizon. He requests that you go there immediately, to attempt to stop the attack, but also, and more importantly, to gain a better understanding of the attacks and to research a way to oppose new ones.
Assemble a team (2) Edit
Continue assembling a team with new dossiers from the Illusive Man.
This part of the main mission requires you to recruit additional squad members, and the following dossiers are added: Dossier: The Assassin, Dossier: Tali and Dossier: The Justicar. It ends when the Illusive Man decides to speak with you again in the Normandy's comm room to give the mission below.
Investigate Collector Ship Edit
Board and investigate a derelict Collector vessel for valuable intel.
The Collector Ship mission unlocks at the fulfillment of a complicated set of triggers since Horizon. See here for specifics. Once triggered, you cannot begin any other mission until this one is complete.
You are sent to investigate a disabled Collector ship in order to determine how to use the Omega 4 Relay without being destroyed.
You leave after EDI hacks into the mainframe of the ship and discovers that Collectors use a Reaper IFF to get past the Omega 4 Relay.
Acquire Reaper IFF Edit
You travel to a dead Reaper to get its IFF transponder. When you arrive you discover that it is not dead but mostly disabled, and as you fight your way to the core and the IFF you get help from an unexpected source.
You obtain the IFF, kill the Reaper, and have the option to recruit a new member to your party.
Await IFF Installation Edit
Complete recruitment and N7 missions while the Normandy crew installs the Reaper IFF.
After you have acquired the IFF, Commander Shepard has to wait until the installation has been completed.
Note: The time limit for Reaper IFF installation is unpredictable. In some cases, where all previous missions have been completed prior to the IFF mission, the IFF can be activated immediately after the IFF mission. In this situation, it is important to activate Legion prior to accessing the Galaxy Map. Otherwise, it is impossible to perform Legion's loyalty mission and also save the Normandy crew. In other cases, the player is allowed many more missions to be completed before the IFF is installed. More confirmation is needed.
Once the IFF is installed, EDI will inform the Commander that the IFF is almost ready. Accessing the Galaxy Map will trigger an irreversible event where the Collectors will ambush the Normandy.
Save the Ship Edit
As you take hold of Joker you will see floor lights throughout the ship guiding you to your destination. He doesn't have any weapons and can only hobble, so you have no choice but to ignore your crewmates while they're getting manhandled by the Collectors. Loitering near any Collector when they've finished with the crew will cause a cutscene and a game over. There are no save points at any point; you start again at the bridge if you screw up.
From the bridge the first destination is through ducts inside Mordin's Tech Lab. A Praetorian will come out from the elevator and turn its attention on Crewman Hadley and others so make use of the distraction. You will emerge in Deck 3 in Thane's quarters and Crewman Hawthorne pledges to protect you. He gets thrown across the room shortly afterward and you will witness Kelly Chambers being forced into the elevator by a Scion. There is another Scion in the Crew Deck so there's no reason for you to linger; hurry up over to EDI's AI Core to release her locks.
When that's done take the maintenance shaft to the engineering room on deck 4. Joker will emerge at the engineering subdeck and will have to take the stairs up. If you take the floor-lighted path to the starboard side (Joker's inital right), an ominous shadow fills the subdeck stairs and you have to wait for it to pass before proceeding. You only have one shot at this: the hostile will return and catch you on the next pass wherever you are. Tip: don't follow the lights this time and go left for an immediately clear path. When you've activated the console next to Tali's usual spot, control over Joker is over and the subsequent cutscenes deal with EDI taking care of the problem.
In the immediate aftermath you learn that the entire crew except for Joker had been abducted. You are now at a major decision point: either head to the Omega 4 Relay immediately, or finish any remaining assignments. If you choose to go immediately, you will save the entire crew. If you do 1 to 3 assignments, then you will lose half the crew, including Kelly Chambers. If you do 4 or more assignments, then you will lose the entire crew except for Doctor Chakwas.
Note: If the player does not wish to wait for the IFF to be installed, and has completed all of the missions they would like to do, simply flying to the Omega 4 Relay and activating it will begin the next part of the mission.
Use Omega 4 Relay Edit
Use the Omega 4 relay to begin the final assault upon the Collector base.
This is the point of no return. Before you use the relay, make sure that every team member is loyal and the Normandy's fully upgraded with shielding, armor and the Thanix cannon. If your ship is not fully upgraded or some of your team members are not loyal, parts of the crew might die during the Suicide Mission.
Illusive Man Briefing Pre-Relay Edit
The Illusive Man will brief Shepard (who is in full armor) and tell you that he doesn’t know what to expect on the other side. You will then be treated to a long cutscene where your decisions on ship upgrades will play out.
The Normandy Attacked Edit
The enormous wreckage field into which you emerge testifies to the number of ships which have tried, unsuccessfully, to travel through the Omega 4 relay. Joker manages to maneuver the Normandy around the debris but EDI will warn that there are enemy vessels approaching. Joker takes evasive maneuvers as they open fire on the Normandy's upper hull. If you failed to upgrade the Normandy's armor, then an Oculus laser will penetrate the Normandy's hull and kill Jack.
A pursuing Oculus will punch through into the Normandy's cargo hold. Shepard takes two squadmates down to deal with it. Shooting from cover, keeping your squad mates in cover, and frequently changing position tends to be the best tactics, as the Oculus will constantly pursue you and will also try to flank you. Be careful of the large number of explosive canisters around as they will not affect the Oculus but they can be deadly to you and your squadmates.
For more detailed information on winning this battle, see Oculus#Tactics.
About halfway through the battle a cutscene will play where Joker has to lose the remaining Oculus chasing the Normandy by sending the Normandy through a field of debris. If you didn’t upgrade the Normandy's kinetic barriers, you will lose a squadmate here when the Normandy's drive core overloads. Eventually Joker emerges from the debris field with the remaining Oculus destroyed, save for one which re-enters the cargo hold. Joker comments that "It's up to Shepard." You will return to the cargo hold (now standing on the opposite side from where you started earlier) where the Oculus returns and continues the battle, with full armor, regardless of how much damage you inflicted before the cutscene. There is a med-kit available at one end of the room. Once the Oculus is destroyed Joker will call you back up to the cockpit when the Normandy is exiting the debris field.
The Collector Base will come into view and it launches an old friend - the Collector Cruiser - which turns to face the Normandy. If you upgraded the Normandy's weaponry, then the Normandy will easily destroy the Collector Cruiser at range. If not, the Normandy must engage it at point blank range with conventional weaponry and the ensuing dogfight will lead you to lose a squadmate.
Once the Collector Cruiser is destroyed, the resulting explosion overloads the Normandy's systems and sends the Normandy in a crash-landing onto the exterior of the Collector base. Shepard asks if the Collectors can detect them, and EDI replies that this is unlikely because of the lack of an internal security grid - the Collectors probably did not expect anyone to get this far. It is time to infiltrate the base to stop the Collectors, once and for all.
Defeat the Collectors Edit
Destroy the Collectors once and for all.
The Normandy has crash-landed on the Collector base's hull: now you have to go in and destroy it. This mission varies by who is in your party and if you gained their loyalty by doing their side missions. At the end of the mission you finally find out why the Collectors were abducting humans.
You kill the Collectors and either Shepard or Joker talks with the Illusive Man one last time. This conversation varies based on your final decision (the sequel's version of conversation after the Battle of the Citadel).
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