In the episode "Beetle Mania", when several of Beetle's felonies are shown, one of the scenes shown is Beetle freeing MODOK from prison. His only major role took place in "Contest of Champions (Part 3)", where he is a prisoner of the Grandmaster.
MODOK appears as an ally of Red Skull in in "The Avengers Initiative" where he helps Red Skull by disabling Iron Man and capturing Cptain America at the Statue of Liberty. While in a HYDRA Base in Antarctica, MODOK operated a machine that would swap Red Skull's mind with Captain America's but the Avengers invaded the base and undid the body swap. MODOK gets away with Red Skull who swipes Iron Man's armor. When the Avengers regroup at Avengers Mansion, MODOK uses microbots to control the bodies of Captain America, Black Widow, Falcon, Hawkeye, Hulk, and Thor while Red Skull targets the Arc Reactor in Avengers Mansion. Iron Man figures out how the microbots work and frees everyone from the microbots control leaving Hulk to beat up MODOK. MODOK gets away with Red Skull after Hulk, Thor, and Falcon sent the detonating Arc Reactor higher in the sky so that it wouldn't destroy Manhattan. On Red Skull's submarine, MODOK witnesses Red Skull sending a message to every supervillain to join his Cabal in a plan to destroy the Avengers.