Perhaps the most important point for me is the fact that just before you 'wake up' to enter the beam, you get the radio chatter saying the entire Hammer force is destroyed and that no one made it there, including what should have been your squad mates who are seen to escape in the Normandy to the new planet. Add on the fact that in the 'Shepard survives' ending he's in his armour (as opposed to not in armour in the ending build up) in what is clearly London rubble as opposed to the Citadel...then this theory actually begins to make an odd amount of sense. The fact that Bioware have suggested that the fan base has missed a lot also adds to this.
The opening mission of the game with the disappearing child in the vent (only to reappear suddenly on the shuttle with nobody actually noticing him) + the dream sequences also suggests that this is a figment of Shepards imagination. The point being that he's spent so much time around Reaper tech (including EDI's new body and other parts of the Normandy) that it's fully possible that he's suffered some level of indoctrination. Vega even hints that there's something odd about the refitted Normandy. The fact that ME3 goes out of it's way to make clear that indoctrination can occur using adrenaline, as opposed to (of which there would be ample amount in high stress situations) just furthers the theory.
The Indoctrination Codex describes the exact kind of dream that Shepard is having + the headaches he describes, also the feeling about the ship that Vega is getting. Suggesting that Shepard is actually suffering from this all along.
INDOCTRINATION
Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infasonic and ultrasonic noise, and other subliminal methods. The Reaper's resulting control over the limbic system leaves the victim highly susceptible to its suggestions.
Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears. As time pases, they have feelings of "being watched" and hallucinations of "ghostly" presences. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signals, manifesting as "alien" voices in the mind.
Indoctrination can create perfect deep cover agents. A Reaper's "suggestions" can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe. Should a Reaper subvert a well-placed political or military leader, the resulting chasos can bring down nations.
Long-term physical effects of the manipulation are unstable. Higher mental functioning mental functioning decays, ultimately leaving the victim a gibbering animal. Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years.
Bioware also hinted at Shepard having to deal with indoctrination in ME3 in the lead up to the game.
The final post credit scene with the Grandpa/Grandson also blatantly spells it out for you. That planet does not even look close to the one the Normandy crashed on. They pretty much throw it in your face that there is more to come.
A nice hint from the community manager:
o1striker
@JessicaMerizan Seeing how shep only sees the kid in his dreams(besides the beginning), its all a dream at the end isn't it?
Jessica Merizan
@o1striker that's kind of how I interpreted it as a dying hallucination, but I'm not a dev so I don't know what was intended.
The final battle is a battle for Sherpards mind. The destroy option, whilst being presented as the renegade option is the option the leads to Shepards survival and ultimately the battle to win his mind. If you pick the other endings, that means the reapers win.
http://www.youtube.com/watch?v=RW_8qLPQrIc (Shepard lives)
