As much as I enjoy the Indoctrination Theory, I can't help but remember the following;
- If commander sheperd is in Control of the Reapers, there's a damn good chance they can rebuild relays. Also; sentient peace as dictated by Shepard's now Reaper-infused will.
- If Commander Shepmerged all organic and synthetic life, the infinite intelligence that would create could again, build the relays.
- If Commander Sheperd destroyed the reapers, then there are dead reapers laying on every major planet in the galaxy, that no longer indoctrinate, hence reverse engineering is possible.
Still, a really cool idea, and I hope it's legit. The implications of Bioware indoctrinating millions so effectively is.. exciting. :)
e/ the aforementioned points also assumes that MExplosions didn't wipe out all intelligent life in the process