Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infrasonic and ultrasonic noise, and other subliminal methods. The Reaper's resulting control over the limbic system leaves the victim highly susceptible to its suggestions.

Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears. As time passes, they have feelings of "being watched" and hallucinations of "ghostly" presences. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signals, manifesting as "alien" voices in the mind.

Indoctrination can create perfect deep cover agents. A Reaper's "suggestions" can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe. Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations.

Long-term physical effects of the manipulation are unsustainable. Higher mental functioning decays, ultimately leaving the victim a gibbering animal. Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years.