Shaggy & Scooby-Doo Get a Clue! (2006)

S02E03 Inside Job

Upon discovering that Dr. Phibes has ingested a significant amount of the latest nano-tech formula, Shaggy and Scooby realize they need to act fast. They scramble to come up with a strategy to eliminate all the nano-bots from his system before he transforms into an unstoppable force.