User blog comment:Ygrain/EDI and the geth: their purpose in the story?/@comment-4950455-20120723200943

I think it's worth noting that whether the Reapers can truly be said to "live" in Control is a highly questionable one. As I understand it, Shepard is basically overwriting their personalities with his/her own. The Reapers may still be physically around, but I'm not sure if any trace of their original mentalities is.

Of course, the possibility of Shepringer going down the same road as his/her predecessor poses a problem of its own, and while I ultimately disagreed (at least with my Paragon Shep) there's a case to be made that the Reapers are too dangerous to be allowed to exist in any form whatsoever. But I don't think it's accurate to lump Synthesis and Control together as endings where the Reapers "live".