Mario received a letter from Princess Peach that said "Please help me find the treasure" and came to "Villain Town". But there was no trace of Princess Brigitte in the area.

In order to get clues about Princess Peach's whereabouts, Mario visited Professor Frankli, who has been studying treasures for a long time in the town. He learned from him that the "Thousand-Year Door" can lead to the location of the treasure, but he must first collect 7 "Stars" Stone" can open the door.

"If you investigate the treasure, you will meet Princess Peach!" Mario, who judged this, embarked on an adventure to find the Star Stone in the paper world with Christian, whom he met in the town. Wherever the adventure goes, there are various developments such as giant flying dragons, residents suddenly turning into pigs, and cases happening on the train.