Like the Subspace Emissary, this is a long story arc in which acts 63 of 65 characters in the game. However, there are some differences between this and the story mode in Brawl: here places and enemies are directly token from Nintendo games, there aren't stickers; instead there are the power-ups from Smash Tour and Smash Run except for Arms power-up because item don't appear in this mode and grabs, throws, Koopa Klaw and Inhales can act normally against enemies.
Prologue: This is the end
Bowser, Bowser Jr., Koopalings, Boo, King K. Rool, Wario, Ridley, Ganondorf, Skull Kid and Meta Knight are all together, in front of a column of light. Suddenly from the column appears Loptr. He shows to the villains Master Hand and Crazy Hand. They are chained so the villains understand the power of Loptr. He shows to the villain where to go and what to do.
- Playable characters: none.
- Enemies: none.
- Joins the party: none.
Chapter I: The last day of Mushroom Kingdom
Mario, Luigi, Peach and a Toad are walking on Princess Peach's Castle when Luigi sees the Halberd flying. Bowser comes out from the spaceship and with him come Koopas, Goombas, Waddle Dees and Doos. After defeat them, Bowser throws a halo to Mario but Luigi saves his brother. The halo teleports Luigi away and Mario is really angry. Bowser jumps upward and leaves Mario and Peach with the first boss: Gobblegut! Mario and Peach have to defeat him and, once they did this, Matthew appears and calls them to go away.
- Playable characters: Mario, Luigi, Peach.
- Enemies: Koopa, Goomba, Waddle Dee, Waddle Doo.
- Boss: Gooblegut.
- Join the party: Mario, Peach, Matthew.
Chapter II: Space is dying
From the Halberd, takes off a missile to the space. Samus sees this and calls help but it appears that the villain closed the communications. So she leaves to chase the missile, which explodes on Brinstar. Samus goes seeing what happened but appears Ridley, who summons some aliens. Samus defeats them but Ridley destroys the gunship and leaves. Samus is left alone on the planet.
- Playable characters: Samus.
- Enemies: Reo, Geemer, Kihunter, Metroid.
- Joins the party: Samus.