The Leader appears as the supplier of Annihilus' mind-control technology and the true catalyst behind Annihilus' gateway to Earth. He was the one who planted Skaar onto Hulk's team in order to learn about them in exchange that the Leader tells Skaar about his past. Skaar attempted to object, but the Leader silences him if he ever wants to learn the truth of his existence, unaware that Hulk was watching the conversation.
The Leader appears in the episode "Contest of Champions" Part 3, as an unlikely ally to Spider-Man, Agent Venom, and Iron Spider. He gets Spider-Man to release him and "help" him free the trapped people of the Grandmaster's ship. After freeing the civilian hostages instead further helping Spider-Man and his team, he jumped into the transporter ray and escaped with the people.
The Leader appeared in the episode "Building the Perfect Weapon". He was stealing technology from a A.I.M. facility and unleashing Ultimo on the Avengers. After seeing how the Red Hulk made so much damage, he devised a way to turn Red Hulk into a weapon and keep the Avengers from stopping him. By playing into Red Hulk's rage and massive ego, he is able separate Red Hulk from the team and capture him into a Gamma Charger where he transforms him into an indestructible weapon. In the following episode "World War Hulk". the Leader had some control over Red Hulk but as the battle intensified Leader lost control and got knocked out by the rampaging giant. There were no signs of the Leader after the battle finished.
