I've wondered this for a while now, and right now I'm playing Arrival and the Doctor says 'even long dead Reapers hold power'.
Now we know that 'long dead Reaper' has indoctrinated her, so wouldn't the wreckage of Sovereign have done the same to the Citadel? Shouldn't it be full of sleeper agents? What about the parts taken away for the black market?
Forgive me if this has been covered in-game in ME3, but I'm not remembering anything being said about it. 
I can think of two possible reasons:
A: The council, even though they didn't believe that Sovereign wasn't a Geth ship, were able to be persuaded that indoctrination was a real threat, and thus Sovereign's remains were locked away safely.
B: Reapers have to be mostly intact for indoctrination to work correctly. (That would make sense, Indoctrination involves manipulating electric fields and infrasound, it's not just "space magic" that can emanate from any Reaper tech, it needs dedicated hardware to work.) Since Sovereign was broken into pieces rather than left relatively intact like the Leviathan of Dis or the derelict Reaper, it wasn't able to use its post-mortem indoctrination abilities.
Or... the Keepers 'stole' much of Sovereign's remains and broke them down to be recycled, thus eliminating the indoctrination effect. OR, and this is much more likely, the Citadel itself already emits an indoctrination field and the Catalyst subtly encourages things like laws against AI and discourages things like, you know, believing there's a bunch of genocidal AI-driven starships out in dark space waiting to annihilate galactic civilization when it gets to the point said civilizations might be able to challenge the Reapers.
Just saying.
I can think of two possible reasons:
A: The council, even though they didn't believe that Sovereign wasn't a Geth ship, were able to be persuaded that indoctrination was a real threat, and thus Sovereign's remains were locked away safely.
B: Reapers have to be mostly intact for indoctrination to work correctly. (That would make sense, Indoctrination involves manipulating electric fields and infrasound, it's not just "space magic" that can emanate from any Reaper tech, it needs dedicated hardware to work.) Since Sovereign was broken into pieces rather than left relatively intact like the Leviathan of Dis or the derelict Reaper, it wasn't able to use its post-mortem indoctrination abilities.
Option A sounds plausible, and I've wondered how much you'd actually need to indoctrinate someone. Seems like a dead reaper never really dies.
Or... the Keepers 'stole' much of Sovereign's remains and broke them down to be recycled, thus eliminating the indoctrination effect. OR, and this is much more likely, the Citadel itself already emits an indoctrination field and the Catalyst subtly encourages things like laws against AI and discourages things like, you know, believing there's a bunch of genocidal AI-driven starships out in dark space waiting to annihilate galactic civilization when it gets to the point said civilizations might be able to challenge the Reapers.
Just saying.
Yeah, I guess the Keepers could've cleaned it all up.
Omg. 
So the Council being a bag of d**** is actually because they're mildly indoctrinated?? I could believe that. 
Also means Bryson never had to worry about being indoctrinated even though he had some barrier that shielded the piece of Sovereign in his office.
Sovereign blew up in numerous pieces. No chance of indoctrination. Derelict reaper was intact mostly. Its core still working that led to the Cerberus scientists to be indoctrinated. The same with the Batarians that found Leviathan of Dis
Why do you think that the council are so useless? Reaper indoctrination is the answer.
Looking at the Reaper issue from the Council's point of view, there's really not much that they can *do*, which is why they don't do anything. They need evidence and a practical course to follow before they can commit to action.
The problem with the Council isn't that they don't do anything, because without a course of action to follow, there's nothing they *can* do. The real problem is that they are actively dismissive of the threat and act to obstruct and harangue Shepard instead of behaving like actual politicians do.
The Council gets all the evidence they need that there is a threat in Mass Effect. But because Mac Walters and Casey Hudson didn't want to tell the story along the lines that Drew Karpyshyn started, because they wanted a more action shooty game with Commander Shootmons and more TV soap opera drama, they hit the giant reset button at the beginning of Mass Effect 2 and hammered it a few more times just in case, in order to destroy the previous course of the story.
B: Reapers have to be mostly intact for indoctrination to work correctly. (That would make sense, Indoctrination involves manipulating electric fields and infrasound, it's not just "space magic" that can emanate from any Reaper tech, it needs dedicated hardware to work.) Since Sovereign was broken into pieces rather than left relatively intact like the Leviathan of Dis or the derelict Reaper, it wasn't able to use its post-mortem indoctrination abilities.
I seem to remember that even small pieces of Reaper hardware could be dangerous for organics? There were several instances throughout the trilogy where organics seemed to treat Reaper remains with great care and artifacts were often contained in order to protect scientists against indoctrination.
I don't think a Reaper have to be intact in order to have an effect on organic minds. However, I guess a non-intact Reaper couldn't directly facilitate the indoctrination process, such as in the case of Sovereign indoctrinating Saren.
Why do you think that the council are so useless? Reaper indoctrination is the answer.
Unlikely, but interesting.
Looking at the Reaper issue from the Council's point of view, there's really not much that they can *do*, which is why they don't do anything. They need evidence and a practical course to follow before they can commit to action.
The Council gets all the evidence they need that there is a threat in Mass Effect. But because Mac Walters and Casey Hudson didn't want to tell the story along the lines that Drew Karpyshyn started, because they wanted a more action shooty game with Commander Shootmons and more TV soap opera drama, they hit the giant reset button at the beginning of Mass Effect 2 and hammered it a few more times just in case, in order to destroy the previous course of the story.
I agree that the council couldn't just start a massive interstellar re-armament project without conclusive evidence of a Reaper threat.
The last part is depressing if true. I've heard it several times before that when DK left the project, the franchise changed direction.. and not for the better. This underscores the importance of having a really talented writer on-board and actually allowing them to complete their work. The Mass Effect trilogy would've been even better if DK hadn't left the project prematurely .
There is no answer to your question. Mass Effect has never had a truly cohesive and competently written story where you're not constantly asking questions about logic or character motivations, so it falls onto you to just make up your own head canon. Why not? It wasn't important enough for the paid writing staff to come up with some excuse so really your made up BS is just as valid as anyone else's.
Does the game tried explaining the whole indoctrination even scientifically? From ME1, they emit some kind of signal that could alter the brainwaves after a prolonged period. But that alone don't explain why Normandy aren't affected so I assume they also use airborne nanites and they infect vulnerable organics and cross between the blood-brain barrier. Although it need to stay active for a period while Shepard and the crew aren't long enough to get exposed..... or I just give up and play it at being space magic.
Proximity matters. Length of exposure matters.
In ME, Rana Thanoptis can give Shepard an overview of indoctrination. There are technical bits to this explanation and in various novels, indoctrination is also revealed to be an effect of Reaper nanides; the same nanides that convert people into husks.
This makes Shepard's *three day* exposure to Object Rho and proximity to Object Rho a bit of a problem. It doesn't matter how 'strong-willed' a character is. Indoctrination starts with a physical infection by technological means and there's no amount of strong will that can fight that off.
But the writers of ME 2 and ME 3 didn't care about piddling little details like that, it would just get in the way of Commander Shootmons shooting mons. So they ignore it completely.
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