He's being indoctrinated!
Read the codex entry entry for indoctrination very very carefully...feelings of being watched...hallucinations...ghostly presences.
I think he was even feeling the effects at the beginning of the game with the little boy, a little boy no one else even seems to see or react to. Sheperd has spent a great deal of time around reapers and reaper tech. He was going to feel the effects sooner or later.
There is a reason why the ending resembles the dream sequences, why what is occurring contradicts why is going on in the background, why the ending is so disjointed. Sheperd is lying on the ground after being zapped by Harbinger, and is being mindscrewed in his moment of weakness. If you chose synthesis or control, the indoctrination works. If you choose destroy, he shakes it off, and you get another sequence of someone in n7 armour waking up amidst the rubble of london.
Now we'll see just what SOB's EA/BW will be if they make the fans pay for the final bit of the game with the real resolution.
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Now speccing 2h sword IRL.