I think the most fascinating thing about this thread for me has been the majority of IT-deniers refusing to provide any counter-argument for why the theory doesn't work. And the only counter-argument that has been cited is esentially "
I don't think the studio that brought us KOTOR can manage good story twists."
Codex entry for indoctrination:
Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infrasonic 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 passes, 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.
Rachni Queen description of indoctrination:
We only heard discordance, songs the color of oily shadows.
If any IT-denier wants to explain what the shadowy ghosts are about in Shepard's dreams, why he gets oily shadows clouding his vision during the ending, why he loses control of his body and mind during the ending, why he gets headaches and hears discordant tones, why he sees a kid that no-one else can see at the start of ME3 that then haunts his dreams and eventually
shows up as the starchild, and why Shepard would be able to resist indoctrination after years spent around Reaper tech and Reapers themselves... then I'm all ears. Please, explain all these effects and animations and events specifically placed into the game. What are they there for? What purpose do they serve if not to hint at the struggle for Shepard's mind after years of Reaper exposure, where so many others have succumbed to indoctrination? Because anyone who thinks the IT doesn't make sense clearly doesn't understand what it's about. The IT does make sense - that much is undeniable. The main game and especially its ending absolutely
doesn't make sense without it, and the only argument I've seen so far is literally
"I think the version of the story that doesn't make sense is more believable, because I have no faith in the team's abilities." Which... okay, I guess? The version of the story
without plot holes seems more likely to me.