How do you figure that? Quite honestly I think the Ark theory makes a lot of sense. Plus it's really the only way ME:A can sidestep the endings in a believable way besides just blatantly ignoring them.
The Ark Theory breaks the lore several times, from us suddenly having intergalactic capabilities where the lore states we do not to going against the story by suddenly having a second, even more complex project despite all resources and the top minds going to the Crucible project which is already straining the galaxy's infrastructure to the point of collapse so if the Ark Theory is true, we doomed the Milky Way even if we defeat the Reapers.
The indoctrination theory has never made sense; People that believe it does are just ignoring blatant evidence. On two separate occasions Vendetta points out that Shepard is not indoctrinated, once on Thessia and again in TIM's office. Not to mention the star child AI at the end says about TIM, "he could never control us because we already controlled him."
Also, the IT is a wayyyy worse ending. It doesn't resolve anything. Shepard is just indoctrinated? Yeah, real great improvement
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It has holes, I agree. Though the version I heard at least has it that the indoctrination doesn't actually happen until the beam run. Which kind of makes sense since we are indoctrinated at least for a moment when we are forced to shoot Anderson. And IT goes with the assumption that the Catalyst is lying to you.
But at least IT just throws the endings away in an attempt to make them unique rather than throwing the lore, the galaxy, and almost all the characters away like the Ark Theory does.