The Indoctrination Theory
Shepard is being indoctrinated the whole time, culminating in the scene with the Citadel. She has constantly interacted with Reaper tech over the past three years, being in the same building as Object Rho for two whole days during Arrival, and keeping the Prothean Artifact that made people go nuts in her own private quarters. Everything after she is hit by the laser blast is a hallucination. Control option is just following what TIM wanted, Synthesis is following what Saren wanted, only the Destroy option, the destroy the Reapers at all costs, the option you've been building up to for the entirety of the series, breaks the indoctrination, which results in Shepard waking up back on earth.
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1. Only when your EMS is high enough to actually survive, when you first meet the Catalyst, does he say "Wake up," instead of "Why are you here?" One of your squadmates is telling you to wake up.
2. Here: dl. dropbox. com/u/26913187/end003_catalyst_m_D_Int. You can clearly hear FemShep's voice behind the Catalyst's. Your subconscious is trying to tell you there is still hope. The voice behind it is MaleShep's if you play a Male Shepard.
3. The pistol you find has an unlimited clip. This could simply be bad writing, but it just seems odd- this is not possible in the real world, lending credence to the idea that it's a dream.
4. Anderson being brought in would make perfect sense for Shep to do subconsciously- she sees him as a father figure. It would not make sense logically, since you hear the radios saying that no one made it through to the beam. In actuality, you are unconscious, and just hearing your own radio. This also goes for Shep herself- when she's staggering down to the beam, someone should have seen her. Obviously they have a point where they can see people going for the beam, since they don't think anyone made it. Yet two people make it in without them noticing?
5. While on the Citadel, during the final scene with TIM, and again with the Catalyst, I believe, you can clearly see traffic going on in the background. This makes zero sense at all. Unless husks have learned to drive air-cars.
6. Here: http:/ www. youtube. com/watch?v=WCXHzbEDK5E Go to 11:55 and watch until the shuttle is destroyed. Notice something? No one ever interacts with the kid. In what situation would adults and marines stand around and just let a kid struggle to pull themselves up onto the shuttle when time is of the essence to get out of there alive? Especially with a Reaper nearby? The kid is not real. He is a product of Shepard's mind- a foothold the Reapers have built through Shep's exposure to Reaper tech.
7. The kid. As stated, he is not real. This explains why Shepard continually dreams about one single kid after going through everything she has been through. There were many kids taken by the Collectors on horizon, and many people she has known personally who have died, (more so if she is Colonist, or Sole Survivor, or both). It also explains the final dream with the kid, where when Shep finally finds him, she sees herself and the kid burn- her subconscious is trying to warn her that following the kid results in her own death.
8. The "breath" scene at the end of the destroy option makes no sense if the endings were real. Shepard cannot possibly survive a fall back to earth, and she is clearly not on the Citadel for two reasons- one, we see it blowing up, specifically the entire central area, where Shepard was, and two- you're surrounded by concrete rubble. The Citadel isn't built of concrete, but London was. What is actually happening is that you are waking up back on earth.
9. The Normandy Crew that step out of the Normandy at the end can be the ones who were in your squad during the final push. This makes no sense at all. They should still be on earth- unless Shepard is just imagining them safely out of the way. Actually, your entire squad should be on earth since you're able to talk with all of them before the final battle.
10. The Normandy herself- why is Joker fleeing the battle? Why did he jump into a Mass Relay? There was no reason to do so since the Reapers were either retreating or destroyed. Again, this only makes sense if Shepard is just projecting because she wants the Normandy and her crew to be safe.
11. The Illusive Man should not be able to get anywhere near the Reaper base. What did he do, just hang around behind your squad the whole time and then jump out and make a run for the beam after Harbinger blew up your assault squad? Not to mention, this would now be three people that somehow made it to the beam despite the radios and the entire Alliance believing no one made it.
12. The game itself only requires 16 GB, when we were told the game would require 25 GB right up until the release date.
13. Building off of #11 and #4, why does Hackett contact Shepard as if he knows she is alive? If everything that took place was real, then the Alliance should believe that Shepard is dead, yet Hackett speaks to her over the console, just assuming Shepard is alive. Not to mention- why is Hackett able to connect to that console? Shep's radio equipment is fried from the laser blast, (as is her shields), so it can't be coming from her, it's clearly coming from the console in the middle of the Citadel. But why can Hackett just transmit directly into it? More importantly, why does he assume Shepard would be in that particular location? Hackett should have no idea that Shep made it to the beam, or even if somehow he assumes she made it, he should have no idea where on the Citadel she is.
14. Animals routinely react with fear to the indoctrinated or those being indoctrinated. Something about them being able to tell that a person is no longer themselves. The hamster you find in ME3, (it's in Jack's old area in the Normandy), is scared to death of you.
15. The Starchild/God-child/Leader of the Reapers lies to you. He tells you that you won't survive the destroy option because you also have synthetic tech in your body. Why, then, do you wake up back on earth? If the Indoctrination theory is correct, this fits perfectly. He is trying to give you another reason not to pick the destroy option.