This mission is acquired automatically after the incident on 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 with the uncovered Collector threat, by any means possible.
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 s/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 Citadel 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: Tali, Dossier: The Assassin 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.
Other missions and assignments can be resumed at this point.
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 addition to your party.
Await IFF Installation EditN7 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. The time limit for Reaper IFF installation varies based on the number of available missions remaining that you have not completed. You may need to complete as many as two or more missions before the IFF will be ready.
Note: If 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.
Once the IFF is installed, EDI will inform the Commander that the IFF is almost ready. Accessing the Galaxy Map for a mission will trigger an irreversible event where the Collectors will ambush the Normandy.
Also note: If you have all missions and assignments complete and spoke with Legion to obtain his loyalty mission prior to accessing the Galaxy Map, landing on Tuchanka, Illium, Omega, or the Citadel will not trigger the ambush until you complete the loyalty mission. If you have any last-minute upgrades or research to complete, do so before you access the Galaxy Map after completing Legion's mission.
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.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, i.e. without completing any missions or assignments, you will save the entire crew. If you do 1 to 3 assignments, you will lose half the crew, including Kelly Chambers. If you do 4 or more assignments, 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 the Normandy is upgraded to your tastes and your team members' loyalties are where you want it. 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.
On activating the relay, the Illusive Man briefs Shepard (who is in full armor) and tells you that he doesn't know what to expect on the other side. You are then treated to a long cutscene where your decisions on ship upgrades play out.
The Normandy Attacked Edit
The enormous wreckage field you emerge in 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 a laser will penetrate the Normandy's hull and kill Jack.
A pursuing Oculus punches through into the Normandy's cargo hold. Shepard takes two squadmates down to deal with it. Tip: Take squadmates who can help you deal with a heavily armored target.
From your starting position, there is a med-kit available to your immediate right. Two med-stations are at the far end. Two boxes of Power Cells can be found about the shuttle bay: one near the right med-station, and another at your near left (by the shielded floor beside gaping wall damage). As usual these will resupply ammo for all of your regular weapons as well as your heavy weapon, and they alternately respawn from time to time.
Tip: There will be multiple refills for both heavy weapon ammo and medi-gel in the upcoming Collector Base mission segments so there is no need to worry about conserving either during this fight.
In the first phase of the battle, you only need to lower the Oculus' armor to about 50% and it will retreat. During this first phase, the Oculus will ignore your squadmates and focus exclusively on Shepard, but you can safely remain behind the control console that you encounter as soon as you enter the shuttle bay: the Oculus will not move behind the console to flank you. Remain in cover while it is firing, then pop up and take it out.
The Oculus returns and continues the battle, with full armor, regardless of how much damage you inflicted before the cutscene.
In the second phase of the battle, you start at the opposite end of the shuttle bay from before, so you will need to find different cover. Also, even if you manage to return to your spot behind the control panel the Oculus will now fly right across it to flank you. There are several tall solid objects running lengthwise down the main area which you can use for cover, and you can dodge around them when the Oculus attempts to flank you, always interposing them between yourself and the Oculus. The Oculus will chase Shepard to begin with, but after being damaged and dodging out the holes in the side of the Normandy a time or two it will tend to start chasing your squadmates instead, making your job a lot easier.
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 comes 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.
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. Just as in the original Mass Effect, you will also be asked to make a very difficult choice that may have serious consequences.
After defeating the Collectors either Shepard or Joker talks with the Illusive Man one last time. This conversation varies based on your final decision (the Mass Effect 2 equivalent of the conversation following the Battle of the Citadel in the first game).
The final missions of Mass Effect 2 are clustered under this journal heading. See the navigation footer below for individual details per section.
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