Indoctrination

"It is the process that Sovereign uses to take control of his adjutants, how it took control of Saren and how it took control of me and my servants."

— Benezia describing the indoctrination.

Indoctrination is the process the Reapers use to corrupt and "brainwash" organic victims into serving them. A signal or energy field (it is currently impossible to determine which generates the effects of indoctrination) is emitted around the Reaper, and those in presence of one will not immediately feel the effects. Depending on the level of exposure to the signal/field or on how much the Reaper exerts itself, the indoctrination can be brute force, subtle, quick or slow. Reapers, when wanting to use thralls as sleeper agents or wishing to disrupt an enemy's command chain, will use indoctrination to corrupt the mind of the organic, making them serve the Reaper. This can manifest itself in the organic as a moral stance or insubordination or simple treason, when in actual fact it is the Reaper metaphorically "pulling the strings". The victim will perceive themselves as perfectly fine, because no matter how subtle or intense the indoctrination, the victim in question is never actually aware they are under Reaper control.

As effective as indoctrination is, it has side effects that diminish its use. Brute force indoctrination can often break the mind of the victim, driving them either insane or reducing them to a mindless husk: either way, neither has any tactical value. The Reaper sometimes has no control over how much exposure the victim has, and other times, although extremely rare, the organic will realize they're being indoctrinated and, in an even more rare case, successfully resist its influence (to date, the only known evidence of this is Captain Shepard). While indoctrination normally only works on organics, the Reapers can use elements of their own code to corrupt machines, as was observed with the geth.