Nanobots are sub-atomic machines, designed to infiltrate technology and rip it apart from the inside out. Their armor is extremely strong, making them nearly indestructible; they are able to survive the equivalent of a nuclear strike. They sometimes use equally microscopic power tools to do their damage. When nanobots infiltrate a robot, they can hijack the robot's control systems and make it do whatever they wish.

Nanobots are employed by the Clotharians. Whether the Clotharians use them against one another is unknown, but Maximum Aldwin sent a batch to Earth as a punishment for VOYAGER 2's accidental photographing of a top-secret Clotharian military base. The nanobots invaded and took over Ida, programming her into a walking bomb that would destroy the city and spread the nanobots over the world. A sufficient swarm was present to ensure that, in the space of seven days, all human technology would have been destroyed.

Fortunately, this swarm was defeated by the Middleman and Wendy Watson. A group of five nanobots were grown to human size, but the Middleman was unconcerned; though indestructible, the nanobots could only destroy technology from the inside out, not the outside in. He planned to build them a "really big circuit to take apart" (which Wendy called a "nanobot habitat").

It is unclear whether any weapons can destroy nanobots, but it is known that Ida's root antivirus system is capable of eradicating them. ("The Boyband Superfan Interrogation")

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