Gonna go ahead and debunk this. Yes, he was indoctrinated. What he thought was helping Shepard, was attempts to help the Reapers. Horizon being used as bait, why pick a world with the VS on it? Picking any colony and making the claim the VS was there would have gotten the same result. Collector Ship? TIM lied blatantly about the Turian distress signal and sent Shepard into a trap that almost got them caught and the Normandy destroyed again.
The Reaper IFF was a mixed bag cause it wasnt going to help anyone in any form unless Shepard died.
TIM: "It's never that simple. You of all people should understand that."
Mordin: "Necessary risk."
TIM brought back Shepard -- from the Reapers' ready grasp, no less -- to fight the Reapers. No indoctrinated thrall would do that. If the player (and by extension, Shepard), is too naiive to realize that the Reaper threat requires Shepard risking his/her life for from time to time, then it's easy to see why some would believe TIM is actually "helping" the Reapers, but it would still be wrong.
TIM's argument for keeping the base instead of wiping it out was the argument of a man who was indoctrinated and looking to make it spread through the rest of his organization.
Cerberus has had, used, and studied Reaper-tech long before the events of Mass Effect 2. So if TIM was just trying to get them all indoctrinated, he did not need the Collector Base. He not only had their tech, but studied it, and new what precautions to take to prevent any of them from getting indoctrinated.
And why? Because Cerberus was set up as an organization to fight the Reapers. He saw visions of them, and warns of an unknown alien threat in the Cerberus manifesto that humanity needs to be armed and ready to fight against. You might notice that Cerberus operatives all agree the Reaper threat is real, even when very few people in the galaxy believe it at all.
Secondly, no, it's not the "argument of a man who was indoctrinated." It's a sound argument from anyone willing to fight the Reapers, knowing that risks must be taken since the odds are not on our side to begin with. Javik himself argues something to that effect in ME3. Also, it is the argument people outside of the game can make, and have made (unless you want to go full IT and accuse the players of being indoctrinated, but you'll rightly be laughed out of this forum).
Now unless you wanna claim that Evolution is full of crap and the writers were lying in official canon material, drop the idea that TIM wasnt indoctrinated.
Getting zapped by a Reaper artifact for a second doesn't make one indoctrinated. Shepard gets zapped by Object Rho and spends two days in its vicinity, but is not indoctrinated. So no, TIM's brief exposure to the Arca Monolith is not enough.
Also, if ME:E was meant to show us TIM is indoctrinated, why don't the ME novels similarly detail Reaper voices inside his head as they do for Paul Grayson?
And more issues yet with this interpretation I haven't gone into here (but have elsewhere):
--> Indoctrination requires days-to-weeks of continous/uninterrupted exposure to Reaper tech to set in. Again, TIM does not stay around the Arca Monolith device very long at all. Shepard spent two days knocked out at The Project, but is fine. A lot of people assert "he wasn't indoctrinated at ME:E, but over the years it was setting in." It doesn't work like that. Indoctrination does not set in over years. It also requires you to be in the presense of some kind of indoctrinating device at all times.
The Codex merely says that the thrall can be sustained for months-to-years, but that assumes they are, in fact, indoctrinated in the first place. No such assumption is safe to make with TIM.
--> TIM's actions undermine the Reapers far more than they could acceptably have allowed of their thrall: stealing Shepard's body from them, wiping out the Collectors and human Reaper, almost figuring out how to take control of them.
He also wouldn't have created that large, multi-billion credit organization committed to stopping the Reapers. Yes, Cerberus was created in large part to fight the Reapers (TIM: "I've been fighting them longer than you can imagine"). The device he touched gave him visions of the Reapers, he just couldn't put his finger on what they were (much like Shepard intially couldn't make sense of the vision from the Prothean Beacon). And the Cerberus manifesto talks about protecting humanity from some dark, alien threat. That's why everyone who works for Cerberus acknowledges the Reaper threat as legitimate, even before the war takes place and most thought them to be a myth.
Note that TIM never says he wants the Reapers destroyed in ME2, just "stopped" ... which doesn't rule out Control.
(...)
--> When TIM implants himself (as seen in a video log at the end of Sanctuary) with Reaper tech, Sanctuary had already happened. The doctor warns against implanting himself, as TIM would then risk losing his mind to the Reapers. That would not make sense if TIM was already indoctrinated (if any tell-tale symptoms existed, a doctor would notice).
*edit 2*
--> Vendetta, the Prothean VI, was programmed to withhold the Crucible information from indoctrinated agents (which he can detect, apparently). Where do we find Vendetta again after he's stolen from us? (Answer: TIM's office).
--> When shot dead in the final, face-to-face confrontation with TIM, you can see his implants power-down (the lights go off) after falling to the floor. His eyes do not similarly power out (credit goes out to Steelcan on this discovery, not I).
Again, this is the same story that ends with Shepard saying (unavoidable): "So (TIM) was right after all." That means they were all wrong about him before, and that would seem to include Shepard's accusation of him being indoctrinated and really just working for the Reapers.
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