User blog comment:Awayorafk/Believe. The Indoctrination Theory./@comment-5916798-20151009123613/@comment-96.255.148.173-20160423151751

Actually, the most pervasive theme throughout the ME trilogy is indoctrination, not "the war between organic life and artificial life." This is all set up first on Eden Prime when your first, jarring experience with indoctrination is fighting husks - rapidly indoctrinated humans. The end of the first mission of the entire trilogy is your hallucination experience with the Prothean beacon. The themes from the very beginning are malicious transformation, betrayal (Saren betraying Nihlus), and mental invasion.

The chief enemies in ME1 are Saren and Benezia, both formerly noble (?) characters now consciously working for evil purposes. The story shows you the most insidious fate as a powerful person working toward an evil goal due to a small kernel of corruption.

Having come directly from watching a fully indoctrinated Saren at the end of ME1, you start ME2 coming to terms with your own salvation through integrated Reaper tech. Thus, you spend all of ME2 not only doubting the trustworthiness of TIM, but also yourself. You even exhibit the same physical scarring and discoloration as Saren did as he was indoctrinated. The final battle with a "human reaper" is a metaphor for this internal conflict - man vs. self.

Finally, in ME3, the Reapers begin their assault on the galaxy in earnest. You, the principle actor in foiling Reaper operations up to this point, begin to build a web throughout all the capable organic species to try to stop them. You are naturally targeted by the Reapers not only for indoctrination, but for the slowest and most insidious indoctrination. There is in-game lore about how the Protheans nearly destroyed the Reapers with the crucible only to be betrayed at the last moment by a faction of Protheans convinced they could use the it to control the Reapers. In the "final battle" on the crucible, you are likewise tempted by both the "control" falsehood which tricked the Protheans (and TIM) and a false "synthesis" temptation which tricked Saren, and presumably was concocted because of the state of the galaxy during this cycle with an independent geth.

My point in writing this is only to show how the themes of the story are most faithfully achieved through the Indoctrination "Theory" (or more accurately, "interpretation"). You may interpret the ending however you like. There's nothing stupid about having plausible alternative interpretations of a work of art. On a more nuts and bolts level, I personally don't think the end of ME3 is all in Shepard's mind while he or she is lying around catatonic. In every other instance of an indoctrinated person either winning or losing a fight against indoctrination, they've been conscious and coherent. My interpretation is that Shepard reaches the beam, boards the crucible and is in a position to activate the catalyst. What the player sees are the severe hallucinations imposed by Harbinger's final and desperate attempt to indoctrinate Shepard. Harbinger cannot deceive Shepard sufficiently to blind him or her to the opportunity to destroy the Reapers, so if the Destroy ending is chosen, the events unfold as depicted in the ending scenes.

To me, all the folks who chose Control or Synthesis surrendered to Harbinger in this last moment of the game, succumbed to indoctrination, and failed the fleet battling outside the crucible. In any other game, you would clearly die fighting the final boss and just reload the game until you won. ME3 players' eyes-open willingness to lose a game and walk away, even stridently defending the choice to do so, is so magnificent and beautifully tragic as to make it the most artistic and meaningful ending to any video game ever.