Parakarry delivers a letter from Princess Peach to Mario's house. It invites Mario and Luigi to the castle. Upon arriving, however, an earthquake begins and the castle falls into a large crack that appears in the ground. Mario sees Princess Peach screaming for help, and dives after her.
The castle fades out of Mario's view, and he crashes into the ground in front of a shop, causing a large explosion of dust. The shopkeeper, Goombianne, comes outside and wonders what happened. She drags the unconscious Mario into her store. Mario wakes up in a bed, where Goombianne asks him what happened. He tells her the story (in a similar way to his story telling in Super Mario RPG). Goombianne tells Mario that he is in Silvertown, which is a town in the north-west outskirts of the Mushroom Kingdom. As they are speaking, the ground suddenly shakes. Heading outside, Mario sees that Bowser has also fallen from the sky. Unlike Mario, he is not knocked unconscious and upon seeing Mario decides that he had something to do with his castle also falling through a crack that appeared in the ground.
After a short boss fight (with Goombianne giving a tutorial on the game's combat system), Bowser swears he will get revenge on Mario and leaves.
Meanwhile Princess Peach and various Toads are panicking as the castle is floating in a black expanse. While exploring the castle, Peach sees a shadowy figure which grabs her and escapes.
Chapter 1 - Travels on the Silver Path
A Koopa runs into town, exhausted, warning everybody that an earthquake happened on the Silver Path leading out of town. Mario and Goombianne go to investigate, often catching quick glances of a shadowy figure following them.
As they travel along the path, defeating various enemies along the way, they suddenly come to a giant crack in the ground like the one the castle fell into. They are about to turn around when suddenly a Bullet Bill comes flying down the path, being chased by a group of Goombas, and they all fall into the crevasse.
The partners in the game are:
- Goombianne: A Goomba who owns an item shop. She is knowledgeable about many subjects, which lets her use tattle to tell Mario about locations, items, people and enemies. All tattle information is recorded in her journal.
- A Bullet Bill - can fly forwards to hit switches and collect items
- A Nokobon - can explode and destroy obstacles
- A Fishin' Boo - can carry Mario across pits and hover over spikes
- Maggy - shrinks Mario so he can fit into tiny areas. Enemies do not notice him but he can still receive damage
- A Baby Blooper - can carry Mario across water
- A Dry Bones - can hide Mario under his bones, hiding him from enemies
- An Amp, who will be optional - reveals hidden items, and also lights up dark areas