In Arcade Mode, each franchise has its own boss to fight. These battles are fought at Stage 10. The following bosses fight certain characters at certain points.
- Mario, Paper Mario, Luigi, and Peach: Count Bleck
- Bowser, Bowser Jr, Fawful: Prince Peasely
- Link, Zelda, Shiek: Demon Beast Ganon
- Yoshi, Kamek: Giant Baby Bowser
- Kirby, King Dedede, Meta Knight: Drawcia
- Marx, Yarn Kirby: Yin Yarn
- Pikachu, Mewtwo, Lucario: Arceus
- Pichu, Jigglypuff, ???: Lance
- Mega Man, Zero, Tron: Dr. Wily
- Lloyd: Mithos
- Sonic, Knuckles: Dr. Eggman
- Marth, Ike: The Black Knight
- Pit, Ice Climbers: Eggplant Wizard*
- = Pit may change when Kid Icarus Uprising is released.