I see that the Indoc theory is making a comeback. I'm sure that anything can make sense when you see it through a lens crafted out of bitterness and denial.
I never knew anything about the ending, other than the outcry against the bad ending. I didn't know it when it was ongoing, so I don't know if the outcry was against plot holes during the last hour of the game, or just the ternary ending system with poor following CGI.
I never understood the popularity of the Indoctrination theory. It's basically an attempt to excuse bad writing.
First time I played through, I did the refuse ending. I felt a bit underwhelmed, because there's basically no ending after it. Indoctrination theory or not, my theory about the catalyst wanting to placate Shepard at the encounter should be a very viable one. I see no reason why someone that has a directive to preserve organic life, but made the Reapers, to ever really give the choice back to the organics.
After the lackluster ending, I went back and started playing through the others. When I did, a lot of questions started coming to my mind. Why did The Harbinger suddenly just leave? Where the fuck did Anderson come from? Anderson appeared in another part of the citadel. Both gave the same recount, but Anderson said it reminded him of Shepard's description of the collector base. That's usually used in literature of a harbinger that this is one mind playing several parts. But I didn't think more about it. What did strike me as very odd, was that Anderson made it to a bridge, and passed it. He made it over as Shepard made it to the bridge. We didn't see him, but there was only one bridge into the control room. The way the whole thing was so linear and just lead up to the plot-device was very hard to swallow too, but at this point I thought this might be what people disliked about the ending.
But, when The Illusive Man entered, I heard the Reaper sounds. I started wondering if this was how indoctrination worked. I thought about coming to NeoGAF and asking about these things, but I found the indoctrination theory before that. I don't get where Anderson came from, but more startling was the fact that when Shepard shot Anderson, both groaned, and then, later, Shepard was shot in the exact same place, with a clear bullet-hole. Last bullet wielding gunman I fought was the Marauder before the beam, and he very distinctly shot me in the shoulder.
I only sat a question mark at this as far as I had gotten, but when I was presented the theory, and saw that the trees from the dreams about the boy was back near the beam, and only back when the alleged dream-sequence started. It's also important to note the clear Reaper presence in the dreams Shepard has. First time I did Destroy, and saw Shepard breath, I most definitely thought that that looked like rubble on Earth. But I still don't believe that Shepard didn't go to the Citadel. I'm not clear about that. I don't think this was just Shepard lying on the ground, totally hallucinating, and I'm not bothered that the Reapers didn't just turn off the beam. That's just plot-convenient.
To me, Reapers had tried indoctrinating Shepard since the meeting with Sovereign. He said turning Shepard would be very useful. Shepard is strong-willed, so it took a lot of trying. I think the Reapers really put all they had into doing it near the end. I think they still let him go to the Citadel, but I don't necessarily believe Anderson and The Illusive Man was there with him. They might just have been the inner conflict in Shepard's head. His gunshot wound, the groan of both Anderson and Shepard, and some other inconsistencies paint a picture more reminiscent of some sort of mind-game going on. It might all have accumulated to try and convince Shepard to do either the control or the synthesis ending. After all, the catalyst actually controls the Reapers. We have to infer some omniscience to it, and its choosing to represent itself as the child, seems to empower that. It might be its attempt to play on all the Reapers did to indoctrinate Shepard.
As I said before, the fact that no one else saw the kid, the kid disappeared and the dreams, fit very clearly with the ingame description of indoctrination. They try to persuade you and break you down with mental images and tricks.
The switching of the renegade and paragon colors also plays nicely into this theory. It just seems more was going on than met the eye, and it would be a bigger coincidence for all these pieces to just fit, than there being no composition behind the plot holes.
Lai Keng kept repeating "evolve or die!", and Saren was super-keen on fusing with synthetics. The persuasive nature of the catalyst to say "this is the obviously better choice" is also problematic. These things fit well. Without knowing anything about the original endings or anything, by my interactions with Leviathan, I figured the AI would likely try to deceive me when I met him, so I shot him in the head.
The indoctrination theory shook me to my core, too. It blew me away as a player. Because the reapers had managed to indoctrinate ME. I was going to choose the synthesize ending. But after having heard about it, I just sat there speechless, because I felt as if the Reapers hadn't indoctrinated Shepard, but had actually indoctrinated me. That was awesome. As in, 'inspiring awe'.
EDIT: Maybe it's just wanting to excuse a poor written ending. Who knows. I'm much more content think it's like that. Maybe that's how indoctrinated I am?! Not really, but it's a fun theory.
