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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 precise mechanics of the indoctrination effect are poorly understood. When they disappeared back through the Citadel relay, the Reapers abandoned their indoctrinated slaves, leaving them to starve or die of exposure. But the Reapers viewed them as disposable. They were taken in by other Protheans as refugees, then betrayed their own people to the machines.

As Vigil explains, indoctrinated slaves from conquered planets were used during the last Reaper incursion as sleeper agents. 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. The effect seems to extend to Reaper artifacts, such as the one brought aboard the MSV Cornucopia that brainwashed her crew. Matriarch Benezia said that even Sovereign's interior serves indoctrination: the strange angles of the rooms are confusing and make you uncertain of yourself. It was first reported to Commander Shepard by farmers on Eden Prime, who claimed there was a 'horrible noise' emanating from Sovereign as it descended. A signal or energy field surrounds the Reaper, which subtly influences the minds of any organic individual in range. Indoctrination is the term used for the 'brainwashing' effect the Reapers and their technology have on organic beings.

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