Mario (or Luigi) and Princess Peach are walking in Mushroom Kingdom until an attack occurs at the Castle. Mario (or Luigi) go to investigate the attack while Bowser, Jr. sneaks up on Peach and kidnaps her. The brother sees the kidnapping and chases Bowser, Jr. Then, there is a battle which the brother loses and turns small while Bowser, Jr. flees.
In every world, Bowser, Jr. will take Peach to a tower and then to a castle. After a boss fight, Junior will taunt at Mario.
In the final battle, Junior and Big Bowser will battle Mario (or Luigi). Bowser, Jr. attacks with his shell technique while Bowser tries to blow fireballs and stomp on him. Mario must reach a switch to destroy Bowser.
In the end while Junior is dragging Big Bowser, Junior will taunt at the DS and continue dragging his father.
- World 1: Mushroom Kingdom
- World 2: The Desert
- World 3: The Ocean (can be skipped by World 4)
- World 4: Soda Jungle (can be skipped by World 3)
- World 5: Snow Land
- World 6: The Mountain (can be skipped by World 7)
- World 7: The Clouds (can be skipped by World 6)
- World 8: Bowser's Castle
- Princess Peach
- Bowser, Jr.
- Dry Bowser
- Thunder Lakitu
- Monty Mole Tank
- Petey Pirhana
- Giant Goomba
- Giant Cheep Cheep
- King Wiggler
- Bowser's Minions
- Bowser, Jr. (Towers and World 8-Castle 2)
- Bowser (World 1-Castle and World 8-Castle 2)
- King Wiggler (World 2-Castle)
- Giant Cheep Cheep (World 3-Castle)
- Giant Goomba (World 4-Castle)
- Petey Piranha (World 5-Castle)
- Monty Mole Tank (World 6-Castle)
- Thunder Lakitu (World 7-Castle)
- Dry Bowser (World 8-Castle)