Indoctrination

'Indoctrination' is the term used for the brainwashing effect the Reaper Sovereign has on organic beings. A signal or an energy field surrounds Sovereign, which influences people's minds. It was first reported to Commander Shepard by farmers on Eden Prime, who claimed there was a horrible noise coming from Sovereign as it descended. Matriarch Benezia said that even Sovereign's interior serves indoctrination: the strange angles of the rooms are confusing and makes you uncertain of yourself. The effect seems to extend to Reaper artifacts, such as the one discovered by Dr. Shu Qian in Mass Effect: Revelation, which soon started influencing his behaviour, or the artifact brought aboard the MSV Cornucopia.

Rana Thanoptis, an asari neuroscientist on Virmire, goes into more detail. She describes indoctrination as a subtle whisper you can't ignore, that compels you to do things without knowing why. Over days, perhaps a week, the subject stops thinking for themselves and just obeys, eventually becoming a mindless servant. That was the fate of Rana's predecessor, who became her first test subject, and the captured salarians who had once been Captain Kirrahe's men. But as Saren discovered during his research into indoctrination at the facility, there is a balance between control and usefulness. The more control Sovereign has over a person, the less capable they become. Saren realised that to keep his mind free of Sovereign's control, he had to make himself an invaluable resource. He believed that Sovereign would allow him a reprieve from indoctrination, because the Reaper needed Saren's mind intact to find the Conduit.

Indoctrination is one of the key weapons of the Reapers; one of Kirrahe's soldiers describes it as a greater threat than a krogan army. As Vigil explains, indoctrinated slaves from conquered planets were used during the last Reaper incursion as sleeper agents. They were taken in by other Protheans as refugees, then betrayed their own people to the machines. But the Reapers viewed them as disposable. When they disappeared back through the Citadel Relay, the Reapers abandoned their indoctrinated slaves, leaving them to starve or die of exposure.

The mental damage from indoctrination is severe and permanent. As Shepard saw, the captured salarians on Virmire had been turned into shambling husks, who either attacked on sight or just stood there waiting for orders. Only people with immense mental strength are able to resist indoctrination, and even then, only for a short time. Matriarch Benezia used her abilities to keep a 'haven' in her mind free of indoctrination, hoping for a chance to use it, but this meant she was effectively trapped in her own mind, watching in horror as she committed atrocities on Saren's orders. She refused Shepard's offer of help in despair, saying "I am not myself, I never will be again." The only person who fully escaped indoctrination's grip was Shiala, but her case was unique and unlikely to be repeated.

Ironically, Sovereign's indoctrination may have led to its undoing. After the attack on Virmire, when Shepard told Saren he had been indoctrinated without realising it, Saren's resolve began to falter and he started questioning what he was doing. Sovereign implanted Saren, and used the implants to influence and control him. Saren became indoctrinated, utterly convinced of Sovereign's cause, but when he died, the Reaper somehow used Saren's implants to 'download' at least a part of itself into him, turning him into a cybernetic creature that Shepard's squad managed to kill. Once the creature was finally dead, Sovereign's shields suddenly went down and the Alliance fleet was able to destroy the Reaper.

Known victims

 * Saren Arterius
 * Matriarch Benezia
 * Shiala
 * Captured salarians from 3rd Battalion STG
 * Unknown numbers of Protheans

Likely victims

 * Dr. Shu Qian
 * Edan Had'dah
 * Crew of MSV Cornucopia