User blog comment:Bluegear93/Mass Effect 3's ending, something came to my mind./@comment-5124423-20120526185117

I think you are right about that. It is highly possible that the real ending was in fact the 'indoctrination theory'. It provides many interesting hints. I also found something more to it. There was a round relic that you find in the Firewalker DLC. Two of the scientists examining Prothean ruins became indoctrinated. Shepard saved the relic and put it on his table in the captain's cabin of the N-SR2. It is likely that Shepard was indoctrinated and that the actual ending should have been him fighting indoctrination. But due to time problems, they had to shorten it drastically.