Days or weeks.
Not minutes or hours.
I still don't see how Shepard can be indoctrinated in the time between when he lost consciousness and when he made his choice.
The only logical way for the theory to make sense IMO is if the start of the indoctrination process was during Arrival or something.
Concept not that Shepard went from 0 to 100 in span of minutes. Harbinger did not suddenly come up with idea. Instead, gradual. On numerical scale, consider that at beginning, Shepard is at 10. Early signs of Indoctrination. Reapers trying, failing, growing frustrated. Growl a lot.
Game continues, pervasiiveness of attempts become worse. Manifest in dreams. By Thessia, Indoctrination reaching dangerous levels, think 60 or 70 of 100, but still not Indoctrinated. Free will resumes.
Finally, battle for Earth. Shepard caught in blast, thrown under rubble. Resolve weakening, becoming desperate. Desperation and near death experience result in Reapers getting best shot. Sequence of events best categorized as 99/100. Final choice determines if Indoctrination works or fails.
Considered to be internal. Illusive Man represents the allure. Anderson represents the will against the Reapers. What do you choose? Philosophical debate with Harbinger, convince yourself it is Catalyst. Way to not wipe out Reapers, save universe. Select Green or Blue option. Fail fight, become indoctrinated.
Select red, resist Indoctrination. Wake up, fight Reapers again. Held the line.
Mentally speaking.