In the episode Apprentice - Part 1 and Apprentice - Part 2, Slade uses the nanoscopic probes as leverage to get Robin to be his apprentice. Slade does so by infecting Starfire, Cyborg, Beast Boy, and Raven with the probes, that are connected to a switch that Slade has attached to his wrist. Whenever Robin disobeyed any of Slade's commands, Slade would press the button on his switch, causing the infected Titans to glow orange and yellow, apparently in great pain. Only when Robin seems to give up, or when he infects himself, does Slade release the Titans, bringing them back to normal but with the nanoprobes still running through their bodies.
They later purge themselves of the probes.