All the characters (apart from Rosalina, Pit and Palutena) are at the Star Festival Carnival infront of Peach's castle. All the characters are seen playing games apart from Peach, KK Slider about to play guitar and Jigglypuff who's about to sing into a microphone on Peach's Castle Balcony. When Peach is about to give a speech, the Castle Grounds gets bombarded. As everyone tries to protect themselves, one of Bowser's airships appears and flies to the castle. Peach, KK and Jigglypuff all stand in fear. Bowser appears and Mario, Link and Zero Suit Samus notice this and run towards the castle (Stage 1: Toad Town Objective: Defeat 35 enemies/Make it to the Castle Playable: Mario, Link and Zero Suit Samus) After making it to the castle, they look up to see Bowser putting the 3 in cages. Bowser's Airship flies off fast and Link tells Donkey Kong to look after Princess Zelda. Then Mario, Link and Zero Suit Samus run off after the airship while others attack the Castle grounds, making everyone run away in fear. Rosalina sees all this from the Comet Observatory and tells Polari that the Observatory is going down to Earth. Suddenly, Ganondorf's minions appear and attack the Observatory. Rosalina prepares to fight. (Stage 2: Comet Observatory Objective: Defeat 20 enemies Playable Characters: Rosalina) After fighting, Rosalina loses control of the Observatory and it crash lands on the Sea of Clouds.
The scene changes to a Town as DK, Zelda and Diddy Kong are running through it. Zelda looks up at a castle as the location is revealed to be Hyrule Castle Town. They continue to run until they get to Hyrule Castle and walk through the doors. Zelda walks to a door with a Triforce Symbol on it as DK and Diddy watch. The door opens to reveal a room with a portal in it. Suddenly, there is a massive rumble as a ship crashes into the top of the castle. Suddenly, enemies start attacking them. (Stage 3: Hyrule Castle Objective: Defeat 30 enemies Playable Characters: DK, Zelda and Diddy Kong) When they have defeated all the enemies, they all walk through the portal.
Luigi, being seperated from everyone else, runs through a forest. He hears a noise and turns around to notice Bowser Jr. in his Koopa Clown. Luigi stares in fear, but then overcomes it to fight Bowser Jr. (Stage 4: The Forest Objective: Defeat Bowser Jr. Playable Characters: Luigi Boss: Bowser Jr.) After defeating Bowser Jr, Jr. flies off his Koopa Clown but pulls out a Dark Cannon and fires it at Luigi, turning him into a trophy. Then, Bowser comes and takes the trophy.
Mario, Link and Zero Suit Samus are running through a desert after the airship. ZSS notices flash out light in a nearby pyramid. She opens the door and sees Pikachu defending himself from enemies. The other 3 help him defend himself. (Stage 5: The Pyramid Objective: Defeat 20 enemies Playable Characters: Mario, Link, ZSS) (Ally: Pikachu) After defeating them all, they team up and run after the airship once again.
The scene changes to space as Fox in his Arwing flies away quickly as he is being chased by an Airship. He then does a loop and ends up behind the Airship. He lands the Arwing on the Airship and gets out of it (Stage 6: Airship Exterior Objective: Make it to the end of the level Playable Character: Fox) After searching the ship, Fox comes to a door. He opens it up to a huge room with loads of cages in. The screen goes blank.
Pit is flying through the clouds, until he notices the wreck of the Comet Observatory. He sees Rosalina fix it and thinks shes an enemy. He flies over to her and prepares to fight her. (Stage 7: Sea of Clouds Objective: Defeat Pit/Rosalina Playable Characters: Rosalina or Pit) After one has defeated the other, they revive the others trophy, realising they're good. They team up and jump onto the now fixed Observatory and continue the journey to Earth.
There is now a portal and Zelda, DK and Diddy Kong step out of it, walking into a cave. Zelda walks over to a fountain that shows an image of Hyrule. DK and Diddy walk over and look in shock as it shows a Subspace bomb being set off in Hyrule and everyone evacuating. They suddenly hear a noise outside the cave and go and explore. (Stage 8: Outer Cave Objective: Get to the end of the level Playable Characters: DK, Zelda, Diddy Kong)
Krystal and Kirby walk through the Mushroom Kingdom, when they find a small campsite near a woodland area. The captain of the Toad Brigade comes out of one of the tents. He explains to both of them about what they are doing there. Then, King K. Rool appears and puts the Leader in the leader in a cage. Kirby and Krystal fight to try and save the Toad. (Stage 9:The Campsite Objective: Defeat King K. Rool Playable Characters: Kirby and Krystal Boss: King K. Rool) After deafeating him, they free the Toad. But as King K. Rool flies through the air after being deafeated, he drops a Subspace bomb. The bomb goes off. Out of the smoke, Krystal and Kirby fly on a Warp Star while the Toads escape in the Starshroom.
Chrom and Marth are practising their fighting skills while Lucina watches. Suddenly, the sky goes red and the Halberd appears. Then Primids appear and the trio get ready to fight (Stage 10: The Forest Playable Characters: Marth, Chrom and Lucina) After defeating them, more appear and they get too tired. They are all suddenly teleported away.
The scene switches to Meta Knight and Yoshi running (and flying) through Toad Town looking for any clues as to who attacked the kingdom and where everyone else went. They notice Kirby and Krystal on the Warp Star and the Toad Brigade fly away. They see the Subspace Bomb and they grab on to the Warp Star and try to fly away but land on the ground. They all start running. (Stage 11: Toad Town Objective: Make it to the end of the level Playable Characters: Yoshi, Meta Knight, Kirby and Krystal) They make it to Peach's Castle. Suddenly, a ship comes and lifts the Castle up, making the water from the moat land on Kirby, while Meta Knight laughs. They all climb up the castle and into the ship, where they notice Tom Nook surrounded with bags of money/bells. Meta Knight walks towards the ships controls and steers it away from the Subspace bomb.
The scene switches to Skyworld and Palutena is looking for Pit. She goes to a fountain and look in it and sees Pit and Rosalina on the Comet Observatory. She then notices they're being chased by a massive fleet of enemy ships. She grabs her scepter and her shield and jumps out of the gates and flies through the air. (Stage 12: The Clouds Objective: Make it to the end of the level Playable Characters: Palutena) Palutena finally catches up with the Observatory and she flies onboard as Pit bows down to her. Rosalina walks over to Palutena as she warns Rosalina about the fleet. The fleet appears and shoots at the Observatory, finally damaging it so much it can't function properly and starts falling to the ground.
The scene switches to a forest area as Greninja and Lucario walk through it. There is a sudden flash of light and it shows the two as trophies. It is revealed it was a possessed Luigi. As he goes to take the trophies, he is shot by lighting. He turns around to see Mario, Link, Zero Suit Samus and Pikachu and they challange him. All of them get ready to fight. (Stage 13: The Forest Objective: Defeat Possessed Luigi Playable Characters: Mario, Link, Zero Suit Samus, Pikachu) After defeating him, shadow bugs come out of his body and he falls to the floor. The essence turns out to be Medusa as she laughs evilly. The four get ready to fight her but Bowser's Airship arrives over head. She teleports on board the ship. The four help Luigi up and revive Greninja and Lucario. The seven team up and continue through the forest.
Fox is in a room full of cages. He looks around until he comes across three cages which contain Princess Peach, KK Slider and Jigglypuff. He breaks them out and they all thank him. Peach walks towards the door and is then surrounded by Primids. Fox, KK and Jigglypuff prepare to fight them off (Stage 14: Airship Interior Objective: Defeat 20 enemies Playable Characters: Fox, Jigglypuff, KK Slider) After saving Peach they all exit the ship and get in Fox's Arwing.
Impa, Captain Falcon and Wii Fit Trainer are walking through the woods, when they hear a loud crash. They run to the sight and find Rosalina, Pit and Palutena. The six greet each other and team up. Suddenly, the sky goes red and Primids appear. Impa draws her Giant Blade and the six get ready to fight. (Stage 15: The Woods Objective 1: Defeat 30 enemies Playable Characaters: Impa, Captain Falcon. Wii Fit Trainer, Rosalina, Pit and Palutena) After defeating the enemies, Ridley appears and attacks Wii Fit Trainer, but she survives. (Objective 2: Defeat Ridley Playable Characters: Impa, Captain Falcon, Wii Fit Trainer, Rosalina, Pit and Palutena Boss: Ridley) After Ridley is defeated, he disappears as the Airship flies over. The six continue through the Woods as Rosalina looks sadly at the Observatory.
Donkey Kong, Zelda and Diddy end up in a field. As the look around, enemies sneak up to them. Zelda notices them and tries to warn the other two. DK and Diddy are turned to trophies. Zelda gets ready to fight. (Stage 16: The Field Objective: Defeat the Enemies Playable Characters: Zelda) After defeating the enemies by herself, she is weak. She has enough power to teleport DK and Diddy out of the field before passing out. The camera zooms out to reveal Ganondorf and his army surrounding Zelda, who is covered by her cloak.
Chrom wakes up in Toad Town. Just as he is about to be engulfed by the Subspace Bomb, a rope ties around him and he is pulled up. He ends up in the Halbred and him, Yoshi, Meta Knight, Krystal, Kirby and Tom Nook team up. Suddenly, Peach's castle (which is still being carried by Halbred) is starting to be released from the ship. They notice to late and the castle is dropped to the ground. Krystal looks out of the window and notices Medusa. She grabs Yoshi, Chrom and Kirby and jumps out of the ship. Meta Knight and Tom look on confused and start to land. When everyone reaches the ground, they get ready to fight her (Stage 17: Outside Toad Town Objective: Defeat Medusa Playable Characters: Chrom, Krystal, Yoshi, Kirby and Kirby) After defeating her, she gives up and teams up with them. They get on board the Halbred and they fly off.
Lucina is seen sitting under a cherry tree, watching the leaves falling and catching them in her hand. A nearby shot is heard and she looks up to see Bullet Bills being fired at her. Before she can react, Lana and Falco destroy them. Lucina stands up and thanks them. However, Wario appears and turns Falco into a trophy. He shoots at Lana, but she dodges. He manages to turn Lucina into a trophy. Lana gets her Book of Sorcery out and prepares to fight him. (Stage 18: Great Cherry Tree Objective: Defeat Wario Characters: Lana) After defeating Wario, Lana revives Lucina. Bowser Jr, appears and steals Falco's trophy. Lana and Lucina run after him, but he flies up to Bowser's airship. Lana notices a fortress nearby and start heading towards it.
Mario's group are in a Battle Fortress. When they head into the Throne Room, Luigi, Pikachu abd Greninja are turned into trophies. Samus notices a person sitting on the throne in black robes. They take the robes off, revealed to be Puppet Zelda. Zelda springs a trap and everyone but Link are trapped. Link prepares to fight her. (Stage 19: Battle Fortress Objective: Defeat Possessed Zelda Character: Link) After weakening her, Zelda summons 2 clones. Link starts attacking one, but they push him back. Suddenly, a portal appears and Samus in her Power Suit steps out. Zero Suit Samus looks at Samus shocked. Samus defeats the fake Zeldas, and Link manages to turn Zelda to her original state. Zant appears on the throne and turns the world into Twilight. Samus frees everyone and Zelda says that if they defeat Zant, the Twilight should disappear. (Objective: Defeat Zant Playable Characters: Mario, Link, Zero Suit Samus, Samus, Zelda, Luigi, Pikachu, Greninja, Lucario) They defeat Zant, but the Twilight stays. Lana and Lucina arrive and everyone teams up. The Samus in the Power Suit explains she's from the future. Zelda tells them they'll have to go to the Twilight Realm. She uses Fayore's Wind and teleports everyone.
