User blog comment:Legionwrex/Why Destroy is the worst ending (besides refusal)./@comment-7167720-20130314204750/@comment-1786741-20130314215136

Indoctrination is explained to some extent and makes sense in the ME universe.

"It is believed that the Reapers generate an electromagnetic field, waves of infrasound and ultrasound, or both in order to stimulate areas of a victim's brain and limbic system. The resulting effect varies depending on the intent of the Reaper: the victim may suffer headaches and hallucinations, have feelings of "being watched" or paranoia, or come to view the Reaper itself with superstitious awe. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signal, manifesting as voices within the victim's mind."

It may be poorly understood, but that's because no one really had a chance to effectively study it. At least it has SOME sort of explanation/theory, compared to the magical green beam that somehow gives organics circuit boards and synthetics organic qualities.