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— Spoilers for Deus Ex: Mankind Divided follow!
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The killswitch are various mechanisms integrated into augmented individuals by Majestic 12 and the Illuminati. It is primarily used as a means to control, and swiftly terminate, compromised individuals. 

Deus Ex[]

In Deus Ex, it is revealed that a killswitch was added to Paul and JC Denton when they received their nano-augmentations. Once this killswitch has been activated, it takes about 24 hours for the person to die. The nano-aug killswitch works by programming the nanites in the targets body to replicate exponentially. It is subtly revealed throughout the story of Deus Ex that both Paul and JC have the Gray Death, and ultimately that their nano-augmentations are the Gray Death. As such it is clear that their killswitches amount to making them suffer the same symptoms as any victim of the disease. Paul describes these symptoms as "not worse than a bad cold". This suggests that it is not quite as severe as suffering from the Gray Death itself. 

Self termination mechanism of a physiopharm agent in action.

Mechanically augmented agents of UNATCO have a similar killswitch; however theirs is activited by a spoken phrase, called a 'killphrase'. Upon utterance of this phrase, the target self destructs almost instantly. They also have what is called a 'self-termination mechanism'. This is essentially a killswitch that activates automatically if an agent is mortally wounded. It has the effect of destroying the agents body (thus removing any evidence of the agent) through an explosion that will also damage nearby hostiles. Physiopharmaceutically augmented agents working for Majestic 12 have the same mechanism, self-terminating explosively when mortally wounded. For some reason, their mechanism does not seem to take effect if the agent is mortally wounded while unconscious. 

Deus Ex: Invisible War[]

In Deus Ex: Invisible War, physiopharmaceutically augmented Illuminati elite troopers exhibit a developed version of 'self-termination mechanism', which causes the subject to dissolve into highly toxic gas if mortally wounded or incapacitated.

Deus Ex: Human Revolution[]

In Deus Ex: Human Revolution, the Illuminati seek to replace the biochip of every mechanically augmented person with one of their own construction. This new biochip would allow them to shut off any and all augmentations within a person, effectively making it a form of killswitch. During the game, this 'killswitch' is used to turn augmented people with the new biochip insane. It is unclear if the killswitch can be used to terminate augmented people; although it is apparent that at the change of a signal, the function of the Illuminati's biochip can change as well. 

One variant of the Deus Ex killswitches appears in the Deus Ex: Human Revolution comic series. It is known as a Dragon-Fire implant and it kills the subject by releasing acid into the subjects's bloodstream. According to Katrina Sutherland, it is a device commonly issued by secret agencies.

Deus Ex: Mankind Divided[]

In Deus Ex: Mankind Divided, Viktor Marchenko has a physical killswitch, known as Damocles' Sword. When activated, it will set off a bomb in his head, killing him immediately and blowing up his body shortly afterward. Marchenko could therefore have set the stonework for later augmented agents as, by 2052, they self-terminate when their killphrase is used.