User blog comment:Ygrain/How the ending might make sense/@comment-4930593-20120617101422

My comment from another thread:

This is the real reason to the ending. The entire last fifteen minutes of play time is all in Shepard's head. It's his subconscious trying to fight to stay alive. This is not Indoctrination, this is his way of processing his life's struggle up until this point and deciding whether or not he did enough or continue to go on fighting.

A little ways back Shepard has to break Reaper control of the Geth by going into the Geth data stream and removing the reaper infected software.. Legion / Geth VI tells him that what he is seeing is his mind's interpretation of what is happening inside of the stream (for example: Shepard only sees Quarians in their biosuits even though they should have been seen as humanoid lifeforms on their homeworld). This viewing interpretation is what Shepard experiences again while he lies dying from Harbinger's beam attack.

Shepard came so close to making it to the transport beam that his mind refuses to give up without playing out the outcome. Everything from that point on is Shepard's mind trying to come to terms with his struggle. He brings in TIM and Anderson because they represent the pro and con of his life thus far. when that is resolved he continues up and meets the child-AI, this is his interpretation of putting it the question into one easy to understand package. Can organic life and artificial life co-exist in the universe. Of the three choices, which has always been Shepard's descision making ability, he can sacrifice his life in order to control the reapers thus ending the war, he can sacrifice his life by allowing both types of lifeforms to exists as one using his interpretation of synthesis, or he can continue the fighting by defying the enemy one last time. It is that third choice Shepard doesn't stop, he continues on and fights thru the flames, this is why we get to see him breathe again back on London.