Episodes that have Mojo Jojo as the primary antagonist, major supporting character, or protagonist.
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- Tagalong
- Telephonies
- The Bare Facts
- The Dog Days of New Townsville
- The Legend of Princess Morbucks
- The Mojo League of Evil
- The Powerpuff Girls Movie
- The Powerpuff Girls Rule!!!
- The Rowdyruff Boys (episode)
- The Rowdyruff Boys (PPGZ episode)
- The Secret of The Powerpuff Girls
- The Wrinklegruff Gals
- Tiara Trouble
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- Total Eclipse of the Kart
- Toy Ploy
- Two Burger-Bots and a Side of Fries