Indoctrination

Indoctrination is the term used for the brainwashing effect the Reapers have on organic beings. A signal or an energy field surrounds the Reaper, 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 make you uncertain of yourself. The effect seems to extend to Reaper artifacts, such as the one brought aboard the MSV Cornucopia that brainwashed her crew.

Indoctrination is one of the most insidious weapons the Reapers have in their arsenal; the salarian lieutenant Ganto Imness 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.

Characteristics
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 of exposure to Sovereign's signal, 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 Arterius 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 realized 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.

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 awaiting 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. When mortally injured on Noveria, a despairing Benezia refused Shepard's offer of help and chose to die, 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; Sovereign's control was supplanted by the Thorian's when she was exchanged for the Cipher, which ended with the Thorian's demise&mdash;a scenario 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 realizing it, Saren's resolve began to falter and he started questioning what he was doing. To keep Saren loyal, Sovereign put cybernetic implants in Saren's body and used those implants to influence and control the former Spectre. Saren found his loyalty to Sovereign's cause greatly strengthened, although he wasn't a brainless slave and could still be reasoned with. When Saren died, the Reaper somehow used the implants to reanimate his corpse and fight Shepard. Because Sovereign was focusing a significant portion of energy to control Saren, the Reaper fell off balance by losing shields and became vulnerable with the destruction of its avatar. With its shields down, the Alliance Navy was able to destroy the Reaper.

Victims

 * Desolas Arterius
 * Ben Hislop
 * Dr. Shu Qian
 * Saren Arterius
 * Matriarch Benezia
 * Shiala
 * Captured salarians from 3rd Infiltration Regiment STG, including Pvt. Menos Avot
 * Collector General
 * Cerberus team on the Derelict Reaper
 * Unknown numbers of Protheans (according to Saren, the Protheans numbered in the trillions, so even 1% indoctrination would be over ten billion), some of whom were later reformatted into Collectors
 * Miners of the N7: Abandoned Mine mission, confirmed in the logs
 * Dr. Amanda Kenson and the members of The Project, not long before the events of Arrival
 * Illusive Man

Comparisons to Thorian enthrallment
The control the Thorian exerts using spores is similar to indoctrination, though the initial conditioning is different. While Reaper indoctrination erodes the psyche until an individual just stops thinking for themselves, the spores allow the Thorian to control its thralls using pain as reinforcement and punishment. If a victim refuses the Thorian's orders, the result is pain so severe that it soon conditions the individual against even considering rebellion; the removal of the pain when they comply serves as further reinforcement. This conditioning allows the Thorian almost complete control of those it enslaves, so that they will even die to protect it.

However, this means that a disciplined mind can resist Thorian enslavement more easily than Reaper indoctrination. Fai Dan and Ian Newstead, for example, are both known to have been able to resist Thorian enslavement to some degree. However, unlike the Reapers, the Thorian is careful not to deliberately injure its thralls; also, Thorian enslavement ceased immediately when the Thorian died, whereas Reaper slaves were left in a permanently indoctrinated state once the Reapers had left.

Other similar effects
In Mass Effect 2 Legion states that the geth heretics (revealed to be a splinter faction of the geth that worship the Reapers and comprise the primary enemies in Mass Effect) either developed or were provided with a computer virus that subtly changed low-level processes of the geth (beneath any "conscious" notice of the higher-level programs), which would eventually lead to an indoctrination of sorts upon the remaining geth that chose not to worship the Reapers. This also implies that the non-organic geth are somehow immune to indoctrination, since the heretic geth sided with Sovereign willingly due to their independent views, and Sovereign did not pursue them further once the main geth collective rejected its offers.