The Master Control Program (MCP) (performed by the late David Warner) is the main antagonist of Jeffrey, Jaden & Friends meet TRON. He was programmed by ENCOM corporation to oversee the game system, but rebelled himself and decided to get rid of the humans, which are termed "users." But he was deleted by TRON, Jaden, Jeffrey and friends.
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- The MCP will return for revenge in Jeffrey, Jaden & Friends' Storm Adventures of Scooby Doo and the Cyber Chase.
- The MCP will become Ed, Double D, Eddy and Darkblade's enemy in The Eds meet TRON. In this crossover, he and Sark are revealed to be members of the Horde of Darkness.