Regardless of player choices up to this point, Commander Shepard is tasked with making a decision regarding the fate of the Collector Base: destroy the base and everything on board, or keep the base intact while eliminating the Collectors so Cerberus can salvage the technology.
Whichever choice the player makes will have consequences in both Mass Effect 2 and 3. Many of these are superficial, affecting the dialogue and cutscenes at the end of Mass Effect 2. The war against the Reapers in Mass Effect 3 is more tangibly impacted by the fate of the Collector Base, though the difference between the two options can be considered negligible in most circumstances.
Shepard is asked by the Illusive Man, Cerberus' enigmatic leader , to preserve the Collector Base for its valuable technology.
Throughout Mass Effect 2 , Cerberus is positioned as a necessary evil - an organization ultimately interested only in preserving and uplifting humanity to a stature above the other alien races. Shepard's rationale behind destroying the base is to rid the galaxy of the site of horrific experimentation on the Collectors' victims, and ensure powerful technology does not find its way into the hands of an organization with questionable motives like Cerberus.
While on the Collector Base, EDI hypothesizes that the Collectors are actually genetically modified Protheans, the historically dominant race annihilated in the last Reaper harvest. Prothean organic material was harvested roughly 50, years ago and used to create the Collectors, indoctrinated slaves of the Reapers.
Much the same is happening to the human colonists who have been taken by the Collectors, though choosing to destroy the base is met with conflicting sentiments from squad mates such as Garrus and Mordin, who point out the scientific value in preserving it.
Taking Mass Effect 2's Paragon route in destroying the Collector Base angers the Illusive Man, who now sits in front of a bright blue star and tells Shepard that the technology destroyed along with the base could have secured human dominance in the Milky Way against the Reapers and beyond.
In a final act of defiance against Cerberus, Shepard tells the Illusive Man that he's no longer calling the shots, and that Shepard is taking the reins to fight against the Reapers.
Instead of blowing up the Collector Base, taking the skin-altering Renegade route has Shepard overload the base's systems with a radiation pulse, killing the Collectors but preserving the base itself. Notably, this video does contain some spoilers, and fans that are new to the trilogy may want to save it for after they have finished their playthroughs.
Furthermore, players that save the Collector Base will receive the Reaper Brain in Mass Effect 3 , while those that destroy it will receive the Reaper Heart. The first of these two War Assets has a Military Strength of , and the latter has a Military Strength of , making them quite comparable.
This is essentially the end of the consequences that come out of the Collector Base decision, and indeed they are not very impactful overall. One final thing to mention is that if a player reaches the end of Mass Effect 3 with an EMS that is below , then they will only have access to one ending choice.
The choice that is available will depend upon whether the Collector Base was kept or destroyed, and thus fans may want to spend a little time reading up on the game's endings. The nascent Reaper is seemingly destroyed when Shepard shatters the feeding tubes that support it, causing it to fall into the depths of the base.
Safe for the moment, Shepard opens a terminal to re-program the base's systems to overload. As Shepard orders the team holding back the Collectors at the door to return to the Normandy, a message comes in from the Illusive Man. He asks Shepard to set the reactor to emit a radiation pulse instead of overloading it.
This way, instead of the station being destroyed, the Collectors in the base would be killed and the technology left intact for Cerberus to use against the Reapers. Depending on Shepard's response, certain squadmates will react. Should the Paragon response be chosen then Garrus , Legion , Zaeed , Grunt , and Mordin will speak in favor of preserving the base, reminding Shepard that it's just data and that destroying it serves no purpose.
If the Renegade response is chosen then Tali , Kasumi , Thane , Jacob , and Jack will disapprove strongly, reminding Shepard of the sick experiments, while Samara and Miranda will have more neutral responses. If the neutral response is chosen then no squadmates will comment. In the end, Shepard makes the decision and sets the reactor.
However, the Human-Reaper climbs out of the pit and engages Shepard and the two squad mates. After the Human-Reaper larva is destroyed once and for all, Shepard hurries back to the Normandy with Seeker swarms and Collectors on their pursuit.
The Normandy races away from the base as the countdown reaches zero, just before Harbinger vows to continue on its plans, and finally ends with the Collectors' destruction. Depending on Shepard's choice at the end of Mass Effect 2, the Collector Base is either preserved for Cerberus or destroyed.
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