There are a few youtube of documentaries on it, but the very very short version is that it was believed that the during the game Shepard was being indoctrinated and by the end of the game he was entirely indoctrinated and that the entire ending was actually playing out in Shepards mind.
There was initial hope that Bioware was going to surprise everyone and confirm the indoctrination theory to be real and then release the real ending a few months afterwards. That obviously didn't happen, but I think it would have been brilliant if it were true.
Watch some of the documentaries you will likely be very impressed with how its put together.
Some of them are wayyyyy too long.
But this one should suffice:
https://www.youtube.com/watch?v=ZZOyeFvnhiI