Mario is at home sleeping when Toad knocks at his house so hard that it falls over. He then enters and shakes Mario but that doesn't do anything, he then yells at Mario which makes him fall out of bed.
Toad turns into Peach who does a screaming like action, he then turns into Bowser who laughs. Mario jumps up and lands on his feet and gathers supplies and then rushes to the pipe with Toad behind him. They enter Toadtown and see it in a ray of disarray.
Music: Bowser's Airship Fortress
Location: Central Toadtown, Paper Mario
Player 1: Mario
Mario jumps on several goombas and koopas and helps free the citizens as they run off-screen. Mario eventually gets to the castle and enters to see Bowser. Mario is about to jump on him when toad appears and locks the gates. Mario turns around to see Jr.
"That pipsqueak Toad is on vacation! Prepare yourself for defeat Mario!"
Jr. gets out his paint-brush and Mario fixes his camp with and angry look.
Music: Mario and Luigi Superstar – Boss
Location: Think Super Mario 64 castle
Player 1: Mario
After Mario defeats Jr. by jumping on his head to knock him out, he turns his attention towards Bowser to see Peach in front of him, but before Mario can move, Bowser presses a button on an odd machine in front of him and an arrow shoots out at Peach. She tries to run, but it catches up with her halfway up the stairs and she is hit in the stomach with an arrow and a trophy stand appears beneath her feet.
The camera pans up close to Mario who does a double take with a shocked reaction and he runs forward, at the same time Bowser grabs Peach by jumping over to the stairs and jumps to one of the two doors leading to the basement. Mario gives chase and sees Bowser going towards the backyard and when Mario is outside he sees Bowser getting away in his koopa clown car. Bowser points towards the ground and Mario sees a bomb being activated by two robots. He's about to stop the bomb when a figure appears hovering over him and makes eye contact with each other. Mario looks at the bomb and quickly gets out of the castle and its range.
As he looks at the town from a cliff, he sees a purple sphere engulf the area, wondering who was the mysterious yellow eyed, red robbed foe, what Bowser did to Peach, if the citizens are in any danger and what happened to his home.