You are Shepard. What reason is there to trust this God-Child? Why believe what is says despite it being completely nonsensical? The fact that he's stronger than the Illusive Man and Saren may well be irrelevant when it comes to indoctrination... we don't know enough to just say "Shepard would have known he was being indoctrinated". The game places us in an area that doesn't makes sense with a character who's reasoning behind why it is apparently the mother-Reaper or whatever doesn't make sense. We can take this and say "yeah, I don't believe it", then choose Destroy indicating that the so-called Catalyst did not change your opinion.
I will, however, concede that Shepard breaking character and accepting what the Catalyst says as fact as yet another plothole. In dreams, you generally accept what you see as real unless you are lucid dreaming. Perhaps this is what is occurring? Shepard is in a state where he cannot question the Catalyst, only accept it as real.
That's precisely my point. I am Shepard and I
don't trust the child. Why then am I forced to accept what he says without question? Your argument, as I understand it, is that since I can choose an ending the Citadel Child cautions against, I can make my skepticism known through action. I'm saying that the inability to first make my skepticism known through dialogue is an example of poor writing. What if I'm skeptical, but not skeptical enough to dive headfirst into something I may regret? I can't question, I can only rebuke. It's frustratingly binary
My point in bringing up Saren and the Illusive Man is that they
did question indoctrination entirely through dialogue. Unable to fully reject it's effects, they then choose to end their own lives. Their experience with indoctrination consists of two parts. A mental sequence in which, through dialogue, they come to realize the extent of their indoctrination, and a physical sequence in which they act on that realization (ending their own lives). Shepard (and thus the player) is only provided with the latter sequence. This is entirely inconsistent with what we know about indoctrination.
This opens more flaws with the Indoc Theory, so I'll just say that it is an issue either way. Shep would not believe the Catalyst if he were not dreaming. Shep in a dream- or indoctrinate-state believing the Catalyst yet still being able to work out he is being indoctrinated doesn't really make sense, unless there is a point of realisation which there is not. Still, it makes more sense that Shep became clearer of mind once being the choice presented itself rather than him just accepting it without even a semblance of logic behind why.
This is another thing. There is no indication that Saren or the Illusive Man were experiencing totally separate realities. The indoctrination only ever played off their pre-existing motivations. Saren, while hating humans, ultimately was a "good guy". Sovereign's manipulation played off of this, but we're never given anything that would indicate Saren was seeing or experiencing things incongruous with reality. He was tricked into believing he could save some by aiding the Reapers. The Illusive Man was himself tricked into believing he could control the Reapers. Again, no indication that he'd been experiencing a wholly different reality, only that the Reapers were telling him what he wanted to hear. Up until this segment, indoctrination has always been a subtle force, slowly edging it's way into the subject's mind. When Shepard experiences it though, we're to believe he concocts an entirely new scenario that's not actually real.
As I've seen it, indoctrination may result in mild hallucinations, seeing ghostly visages, hearing voices, etc. But I think to describe Indoctrination as having all the same qualities as a dream is making an assumption we have little evidence for. So, while some may be more inclined to accept dream logic as reasonable, there's little to indicate that indoctrination shares these qualities.
I feel like much of the evidence for the indoctrination theory is found by working backwards from that assumption, rather than looking at each piece of evidence and deciding what it points to.
We don't know the power of indoctrination. Shepard is extremely strong-willed, but this is technology from those who created the Mass Relays. We have seen indoctrination being momentarily staved-off when convinced by Shep, but never broken.
What reason is there to believe the Catalyst, as I have asked? He is clearly trying to stop you from choosing Destroy. And if you do choose Destroy it is proven that he lied or was incorrect, as Shepard still lives. The hallucination ends when Shepard awakes or when he falls to indoctrination. He is still in a hallucinatory state, regardless of the fact that he broke from it.
I realise I am grasping here, but to be honest I'm not the right person to have this debate with you, as I'm really not good at organising my points and communicating them in a coherent way. Especially as you think the writers just completely lost the plot with the last sequence and think that there is no reason behind the nonsensical things that happen except atrocious writing while I'm trying to make sense of it.
Not permanently broken, but still broken. The Reapers wouldn't allow their thralls to simply off themselves whenever somebody pvssyd with them if they could help it.
I'd also point to the fact that on Thessia the Prothean VI says nothing of indoctrination when approached by Shepard and his team, but totally flips out when the assassin arrives on the scene. It's been established that indoctrination is not a sudden effect, but a gradual one. Why then can the Prothean VI detect indoctrination in Kai Leng, but senses none of it in Shepard. Are we to believe that Shepard was indoctrinated to a extreme degree, far beyond that which was experienced by either Saren or the Illusive Man, in as short a time span as the conduit run?
I'm arguing from the standpoint of what's more likely: That the writers pulled a fast one on the players, but happened to forget established indoctrination lore while ignoring other plot holes and neglecting to include any actual ending? Or that the deadline was coming up, they weren't where they should have been on the schedule, and rushed to turn in a subpar ending?