The original Mass Effect Trilogy revolved around trying to stop a formidable enemy known as the Reapers- a race of sentient spaceships that feel the need to wipe out the most intelligent civilizations every 50,000 years. They prove a dangerous and intimidating opponent, largely because they seem impossible to stop even with all the high-end futuristic technology available to Commander Shepard. In the first game, it took the entire Alliance Fleet just to have a fighting chance against a single reaper, and by Mass Effect 3, an entire army of them is launching a coordinated assault across the galaxy.
The Reapers are such an imposing force that just surviving an encounter with one feels like a victory. Adding to the terror are the numerous tools the reapers have at their disposal, including a talent for abducting other races and mutating them into their own soldiers. Humans get transformed into mindless zombies, Turians get made into strategists, and of course, what was left of the Protheans got turned into the collectors.
But one of the most terrifying things about the reapers is much more subtle. It is not their capacity for mass destruction in seconds or their astonishing durability, nor is it the ways they can mutate familiar races into unrecognizable abominations. It is another ability they can use to great effect- indoctrination. This is a process wherein the reapers can take full control over an individual, and make them act against their own interests. Shepard has to deal with several indoctrinated people over the course of the games, including two major antagonists in the first and third games, and even an entire research station full of them in the "Arrival" DLC for Mass Effect 2. There is even a popular theory that Shepard herself is indoctrinated. While the game's developers debunked that idea, they did admit to finding it intriguing.
6 What is Indoctrination?
Reaper indoctrination is a process that involves transmitting electromagnetic waves into a person's brain and using them to discreetly manipulate the individual. Usually, these signals manifest in the form of barely audible voices in the back of a person's mind, but given sufficient time they are able to take an increasingly strong hold over the victim. If the target tries to resist, the same signals can be used to inflict excruciating headaches as a means of forcing them to comply. Given a sufficient amount of time, the reapers gain complete control over the victim and can make them behave in any way that is needed for the Reapers' goals.
5 Background: Leviathan
The Reapers were originally created by an ancient race known only by the nickname "Leviathan" as a tool to keep subjugated races from destroying themselves with AI technology. The species had a unique ability to observe other planets through spherical artifacts, and when doing so could temporarily possess individuals on those worlds. The target's consciousness would be suppressed while Leviathan took over their body's motor functions. They could then manipulate the person indefinitely, controlling them to do whatever was in Leviathan's interest. Once the required task was accomplished, or the link to Leviathan was destroyed, the person would be released from Leviathan's control with no memory of what they did under its influence.
When the Reapers performed the first harvest on Leviathan, they took inspiration from its ability to control other people, seeing it as a useful tool for future cycles. This became the basis for indoctrination, something the reapers modified into something much more frightening.
4 It is Very Easy to Be Indoctrinated
One of the most unsettling parts of indoctrination is the knowledge that, while the reapers may be selective in who they indoctrinate, it is very easy to fall under its influence. The victim does not even need to be anywhere near a reaper for it to happen. They have the means to transmit the necessary signals from one end of the galaxy to the other, so getting out of range is impossible. Furthermore, all that is required to make indoctrination a serious risk is the presence of reaper technology. Not even anything specific. Any gadget, fragment, or other item created by the reapers can act as a transmitter to anyone in its proximity. Obviously, this makes studying the reapers extremely dangerous.
Fortunately, there are precautions that can be taken to minimize the risk of being indoctrinated while studying reaper technology. The Alliance even has detailed regulations on how to safely approach it. But while those precautions work most of the time, the Reapers have proven resilient enough to sometimes find ways around them.
3 Discretion Is Key
Indoctrination can be done at varying speeds, but it is most effective when done slowly and gradually on an unsuspecting target. Usually, it starts out in the form of barely audible whispers in the back of the mind before growing more intense. This allows the Reapers to start controlling a target without them even knowing they're being controlled. Faster indoctrination is possible, but it runs the risk of causing too much damage before the target can be effectively used. Slow indoctrination can warp the victim's mind to make them more willing to co-operate with the Reapers' interests, often unknowingly.
In the case of both Saren and the Illusive Man, for instance, they were tricked into thinking they had a solution for the Reaper threat and acting in the interests of a greater good while playing into their enemy's hands. The victim can even have their mind warped into thinking they are not being indoctrinated and acting entirely on their own initiative- Saren believed serving Harbinger would spare him the pain of indoctrination, unaware that it was already happening.
2 Tactical Applications
Indoctrination has a variety of applications, but when performed effectively against the right individuals it can be used to devastating effect. This has made it a favorite tactic of the Reapers during their harvests since it can be used to create unaware agents and then turn them on their allies at key moments. One such instance was exploiting the influx of refugees when they were fighting the Protheans- refugees fleeing the reapers were secretly indoctrinated, and then used to sabotage the Prothean forces when granted asylum. But perhaps the most destructive application is to indoctrinate someone in a position of authority, someone with a lot of power and influence. When such a person is indoctrinated it is an easy recipe for chaos and disorganization that easily works in the Reapers' favor.
1 Impossible to Escape
One of the most disturbing parts of indoctrination is a simple realization that it is impossible to cure. There is no way to cut off the Reaper's link to an indoctrinated servant. While the affected person still has some agency, they are subjected to extreme pain if they try to resist the voices in their head. Only one person has been known to have broken her indoctrination- Matriarch Benezia, and even that was only with some considerable mental preparation and only lasted a few minutes.
The reapers will never let go of an indoctrinated victim, and the process causes neural deterioration in the brain. This is one of the reasons why slow indoctrination is preferred, as it can delay long-term brain damage. The process of indoctrination only ends when the victim's higher brain functions have degraded to the point where they are no longer useful. By the time the reapers let go, the victim is essentially braindead.