The indoctrination theory is my head canon. 

Besides, both TIM and Shepard are BOTH indoctrinated before ME3.

Exhibit A)
[IMG]http://img3.wikia.nocookie.net/__cb20130326102450/masseffect/images/a/a5/Jack_Harper_saving_Ben_Hislop_from_Reaper_device.png[/IMG]

^ TIM back when he was Jack Harper trying to save his friend from a Reaper Device. His eyes take on the characteristic glowy Reaper tech look immediately after. This took place shortly after The First Contact War.

Exhibit B) 

[youtube]3ihNRjp3Qjo[/youtube]

Oh look, Shepard just touched a fucking Reaper artifact that indoctrinated everyone you're fighting in that DLC. 

I mean, come on. It doesn't get any more damning than that.