Mass effect 3 ended in a very unorthodox fashion. Plot holes, no final boss fight, anti-climactic, nonsensical; you name it. Regardless, some hated it, some loved it. The group of people in the latter category most likely believe in the Indoctrination Theory (IT). Simply put, the It postulates that the ending sequence (after Harbinger attacks Shepard) is merely a figment of Shepard's mind, and this is where the remainder of the game takes place.

Needless to say, this has been over analyzed to the point of absurdity. every little detail has been picked apart by the loyal fan base, attempting to bring more hints into the light. This is all fine and dandy, but I feel as though the initial message was lost. Not just the IT, but the message Bioware wanted to get across.

We didnt really give the IT a chance... people just complained right off the bat. who knows what Bioware had planned? Just like how they tweeked the script after it was leaked, this demand for an Extended Cut probably threw a wrench in the works. Also, people dont know that the EC was made my a different team than the one that made the original ending. I fear the ending theme of surreal, dream-like, indoctrination attempts may become literal space magic showcases.

Soo after Shepard gets hit by Harbinger, hes unconscious (maybe near death?) and weak minded. Everything that follows is the subconscious struggle to get him to submit to indoctrination. I personally beleive the 'hallucination' begins after Shep passes out the second time, but Ill get to that in a sec. Anderson and TIM supposedly each represent a side of Shepard's psyche, while he must choose between them. This scene is beautiful, because Shepard overcomes (or dies). After this scene, the true test presents itself. Shepard, after watching Anderson die, crawls toward the main control panel, but passes out a few inches short. I know some people that believe THIS is when Shepard goes unconscious. Whatever the case, THIS is where the Indoctrination Theory shines. Keep the following points in mind:

  • The dream sequences/little boy: Obvious symbolism throughout the game, taking place in Shepard's subconscious. The boy (who may or not actually exist) is present in the dreams, always being enveloped in flames. Then in the final dream, we see Shepard with the boy, also being enveloped.... come on people! Dont trust the kid! the appearance of the Catalyst, IMO, implies this HEAVILY. Why else look like the kid? No point. Just make him look like glyph? Nope. Symbolism, people.
  • Shepard's eyes: If synthesis or control is chosen in the end, shepard's eyes are shown to have 'indoctrinated eyes', like the Illusive Man or Saren. Ironically, these two antagonists supported control and synthesis, respectively.
  • Reverse moral colors: This is a subtle yet effective clue that the Reapers are trying to play on Shepard's morals. Destroy (the only reasonable choice) is colored red, the renegade choice, while the two other choices are 'virtuous' and 'best'.
  • Strange/surreal details: These 'plot holes' are actually signs that IT isnt too far off. The lesser of all the points of proof, this point still matters nonetheless.
  • Breath scene: This is THE most important point in the IT, in my opinion. There is NO reason to include this scene otherwise. The devs also DIDNT omit this with the EC, so it was MEANT to be there. For whatever reason that may be...

Now the post decision scenes are shown which are continued fabrications of Shepard's mind. The EC just goes into detail on these choices; still Reaper hallucinations.

  • If Shepard chooses Control or Synthesis, he gets nothing (original ending). In the EC, he believes he made the best choice for the galaxy, with unrealistic consequences. These two choices, regardless of outcome, go against everything he has been fighting for the whole series.
  • If you choose Destroy, you get dead Reapers and no real benefits. EMS score changes this; low makes everyone die and high makes the infamous 'breath scene' be shown right before the credits. Shepard was stessed because he knew he would fail (low) or breaths his first or last breath (high).

This type of thing has been done before, in more ways than one. Examples of this type of thing on other media:

  • Halo 3. Beating 1P Legendary offers a new scene post credits. Master Chief and Cortana, who are both presumed dead post campaign, are seen drifting through space, alive. this type of 'hidden reward scene' is not rare in the videogame world.
  • At the end of the TV series Sopranos, the fate of the main character (who just quit organized crime to enjoy his family) is left unknown. Only the possibilities exist; no guarantees. Shepard waking up may lead you to think "yea, so now what?" but you see, thats the beauty of it. we know our cycle wins the war, as evident by the stargazer scene. How they actually pulled that off post-Shepard-getting -fucked-up is up to the subjective player.