Mario and Luigi, along with Peach and Toad, are walking through the castle garden when Bowser comes! He is in an airship, with a laser aimed at the bros. He yells, "Prepare to time travel!" and zaps them. They disappear. Peach is then grabbed by a Parabro who brings her to Bowser. He flies away, laughing evilly. We then find ourselves in the Cave-shroom Kingdom, a cave-version of the Mushroom Kingdom. We find two cave-brothers, Mariog and Luigar, sitting outside in some kind of garden with Toav. Nearby is a castle made of stone. We hear a scream, and see Bowsek running off with Princess Peaf. The brothers and Toav jump up and run after him.After beating Bowsek and rescuing Peaf, there is a bright flash of light and we switch to Ancient Egypt. Bowraka is running off with Princess Peachapatra, and running close behind are Marijai and Luihem.
After you destroy Bowraka, we are suddenly in Ancient China, seeing Bowsan running off with Emperess Peachus. Mariwan and Luigian are chasing him.
After defeating Bowsan, we switch time periods once again, and find ourselves in the Victorian era with Bowsenstein running off with Princess Peachoria. Mariomas and Luigor run after him, yelling.
After that we finally find ourselves in... the future?! Marinaut and Luig-bot are running with Toadian, an alien toad. Bowsatron is running away from them, flying away with his jetpack and carrying Princess Peachalg, an alien princess.
When you defeat Bowsatron we FINALLY are back in the present, and, thankfully, right near Bowser's castle! The Bros. enter, and find Bowser has collected complex machines from the distant future!!! He traps Luigi in a green orb, but Mario avoids it, and the two begin fighting.
After Mario wins, he zaps Bowser with his own time machine and they all escape just before his castle explodes. After the credits, Bowser is seen stuck in the Stone age, just as a volcano erupts behind him. He looks at the screen and gulps.
- Ironically, Bowraka has an Ankh on his hat, which is a symbol of life.
- Mariomas looks the most like Mario, simply having a different mustache and a stain on his overalls.
- First time Mario's (also Luigi's, Peaches, and Bowser's) ancestors are shown.