Through the Omega 4 Relay, our IFF integrated into the Normandy, we go with no expectation of returning. Prior to this each crew member has requested Shepard take them to complete some unfinished business. If the quest is finished to their satisfaction, they become loyal to Shepard. It’s hinted that their loyalty is important, and it is. Crew without the loyalty boost can die. If Shepard ends up with nobody left, she’ll die, too. Of course, on a first playthrough none of this is understood. Endgame in ME2 is gut-wrenching and nerve-wracking. Each phase of the battle through the Collector base has a specific way someone can fail.
When we get to the final battle we face a humongous human skeleton.
It’s a Reaper powered by the humans the Collectors have been juicing here in their base. Some kind of DNA broth mingles with Reaper technology? It’s not quite clear, and, of course, the whole point is to kill the thing. Whatever it is, it will never reach fruition.
And then it’s time to blow the Collector base. (Does that mean the entire race goes extinct? That question — something so vital to deciding the fate of the Rachni — is never raised.) The Illusive Man patches in and argues vociferously to save the base. A radiation pulse will take out all the Collectors, but the technology of this base can be saved. On the one hand, we have paragon Shepard who objects. Human goo powers this place. It’s abhorrent and morally offensive. On the other hand, we have renegade Shepard who can see the logic of the argument. All of this effort has been about eventually facing the Reapers, a super-powered machine race. Any knowledge gleaned from this base may be our only chance to defeat them. Don’t let the human sacrifice have been in vain.
If Shepard says no, the Illusive Man shows a very dark side of himself. He doesn’t just want to defeat the Reapers. He wants the tech in order to super-power humanity. This is our chance to use advanced knowledge to jump start the human race and control the galaxy. Cerberus has always been about improving humanity by any means necessary. For most of the mission he’s played nice, giving Shepard leeway to decide what’s best. If he’s denied this base, he becomes vicious. He’s only virtual, though, and the decision is Shepard’s.
And that’s where we end. Whoever lived is back on the Normandy with Shepard. Whatever the Illusive Man thinks, he says no more in this game. We stopped the harvesting of human colonies and learned a little bit more about the Reapers. Mostly, we made friends.