Fail Shep awakens on the exterior of the Citadel and comes face to face with a hologram of The Boy who died when he left Vancouver. The hologram introduces itself as the Catalyst, the AI that controls the Reapers.
Long ago, an incredibly advanced species observed that other species kept getting wiped out by their synthetic creations. This species wanted to stop this from happening, and in an act of incredible Genre Blindness, created an AI to solve the problem and gave it all the tools it needed. This AI was the Catalyst.
The Catalyst could only find one solution to the problem it was created to solve: turn every species into Reapers before they can develop synthetics that would wipe them out. The first species to fall to the Catalyst was the one that created it.
tl;dr: "Yo dawg, I hear you're being killed by synthetics, so I made some synthetics to kill you so you won't be killed by synthetics."
That being said, I'm pretty sure the Catalyst's hypocrisy is intentional.
As a side note, the Catalyst is very condescending to a Shepard with Low EMS. It seems insulted that someone so incompetent has nearly managed to derail its plans.
The Catalyst reveals how the Crucible will Destroy the Reapers: it will emit a powerful energy blast that will spread throughout the galaxy using the Mass Relays. This energy will destroy all synthetic life in the galaxy. The Reapers and the Catalyst will be destroyed, but so will the geth, EDI and Fail Shep (Fail Shep has been relying on extensive cybernetic implants to keep him alive ever since Cerberus revived him).
In addition, our low EMS has led to the Crucible being badly damaged before it could dock with the Citadel. As such, the energy will destroy most advanced technology, including the Mass Relays. The destruction of a Mass Relay generates enough energy to wipe out a solar systems. If Fail Shep fires the Crucible, the galaxy is fucked.
There is one other choice: Refuse to fire the Crucible. If Fail Shep does this, the Reapers will wipe out all advanced organic life, but future, more competent cycles may be able to bring the Reapers down for good without screwing over the galaxy.
It boils down to one simple choice: wipe out the vast majority of life in the galaxy, or admit defeat so the less advanced species will survive.
Fail Shep makes his choice.
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