User blog comment:Awayorafk/Believe. The Indoctrination Theory./@comment-186.244.38.243-20131007051246/@comment-1440333-20131007180951

I will, because I'm a bit less controversial.

Indoctrination is the Reaper's way of gaining influence over a person. The process is most successful if performed slowly, requiring prolonged exposure to a Reaper or a Reaper object similar to Object Rho. Husks and Collectors, being indoctrinated creatures themselves, would not be sufficient. Rapid Indoctrination is possible, however it destroys the mind of the subject, making them no use to the Reapers.

The IT argues that Shepard is indoctrinated by the Reapers, and is being used by them to affect the Crucible. This is not possible however as Shepard would be of no use if he had been rapidly indoctrinated. Also Shepard could not possibly have been indoctrinated slowly, as he was never in prolonged contact with any Reaper or Reaper Device. Some people have argued Sovereign was responsible, yet that would also have made Hackett, Joker, the squad and all the Citadel's residents indoctrinated as well, when there is no evidence of that. Others have argued the Derelict Reaper or Object Rho were responsible, yet from the logs on the Reaper its is apparent they have been there for months, and it is possible the Project staff were in a similar situation based merely on the construction of the base alone. Shepard was aboard the Reaper for barely a few hours, and the Project base for less than two days.

It also would seem that the Reapers do not want Shepard indoctrinated - based purely on Harbinger's comments it seems that just like the Illusive Man the Reapers want Shepard intact ideally, but will settle for his death if they must provided they get his body.

TL:dr - Shepard could never have been indoctrinated according to the rules presented in the lore for Indoctrination.