User blog comment:Reptileman778/What is the canon explanation for why you are fighting geth in multiplayer?/@comment-5362182-20120910231514/@comment-5503561-20120911075417

Think of it like this - Geth bodies, as in the physical things you're fighting for the three games, are empty suits of armor. You load in the Geth as a software into them. But instead, what happens here is that raw Reaper code is loaded instead of the Geth.

Basically Reapers are doing massive sockpupetteering.