Biochip

Biochips are a part of all mechanical augmentations distributed in the world at the time of Deus Ex: Human Revolution. These chips control all augmentations in a person's body, from ocular implants to full-body augs.

Deus Ex: Human Revolution
In the game, Adam Jensen, and presumably anyone with mechanical augmentations, has a biochip. The biochip seems to control all non-essential augmentations in the body, such as upgrades and systems like the Typhoon Explosive System.

Later in the game, biochips around the world suffer a glitch that causes pain in the augmented person. The World Health Organization then broadcasts a message stating that the biochips are faulty and should be replaced at a LIMB clinic. The player can then choose to have the biochip replaced, or leave it in and risk further "glitches".

Inside the Omega Ranch facility, Zhao Yun Ru reveals the true purpose of the new biochips - they disable all the augmentations in a person's body when activated by a certain signal. Essentially, the new biochips act as a killswitch. She triggers this switch, disabling Adam Jensen's augmentations if he chose to have his biochip replaced earlier in the game. However, Adam's augs controlling movement of his limbs are not disabled, allowing him to fight Jaron Namir, albeit at a huge disadvantage.

The Illuminati intentionally caused the Glitch for the sole purpose of compelling augmented people into receiving their new biochip. Their intent was to be able to switch mechanical augmentations on and off at will, in order to control augmented individuals. Just as Zhao was able to cripple Adam's abilities in Omega Ranch (providing he got the chip replacement), the Illuminati would hypothetically be capable of doing this to any person on the planet who had their biochip installed. However, the Illuminati never saw their plan realised as one of their own members, Hugh Darrow, sent out a signal which caused every person with the new biochip to experience hallucinations which brought on insanity.