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The story begins as Mario, Link, Pikachu, Kirby, and the rest of the original 12 preform on a stage "Super Smash Bros." Master Hand, who is the group's organizer and manager, watches on. As Mario defeats the "opponents", Master Hand notices that the final boss, Bowser, has not shown up.
As Mario reaches the last act of "Super Smash Bros", Master Hand gets incredibly worried that Bowser still hasn't shown up. Mario reaches the final stage, and Master Hand rushes on stage to take Bowser's place. Mario is a little confused at first, but continues anyway. The crowd loves it, and ever since then Master Hand has been the final "boss" for all their stage shows.
A mysterious man watches in the shadows for all their stage shows. He watches with curiosity as Master Hand battles Mario.
Chapter 1: Your Princess is in Another Castle
The story begins as we get a shot of the "Smash Mansion" owned by the Original 12 and Master Hand. Wii Fit Trainer is doing yoga with Samus and Little Mac, Mario and Luigi are eating spaghetti, and Link and Marth are interlocked in a duel.
Just then Bowser arrives on the castle grounds and grabs Peach who is having tea with Mr. Game and Watch. Mario and Luigi see him take off and head off into his direction, with Samus, Wii Fit Trainer, Little Mac, Link, and Marth following them.
After catching up with Bowser in a canyon, they battle him. As they defeat him, he openly expresses worry with something about being "forgotten". Mario tells him he will not be forgotten, and that such a thought is silly. Bowser agrees and runs back to the Smash Mansion. Meanwhile, a man watches from the shadows.
Chapter 2: Attack of the Cubots
The Smash Bros return to the Smash Mansion, where Master Hand tells them that strange robots have been sighted near the Smash Mansion. Mario and the others return outside, where they find that the robots are trying to break through a barrier.
Peach and Mr. Game and Watch join the Smashers as they defeat the Cubots. During this time, they talk about the formation of the Super Smash Bros and how they didn't initially know Samus was girl, laughing it off all the while.
A huge ship closes in, releasing thousands of Cubots who destroy the Smash Mansion to bits. Master Hand grabs the rest of the Super Smash Bros, and throws them in the Halbred, making sure they get to safety. Master Hand tells Mario and the others to get to sea, as the "Cubots" hate water. While Mario ponders about how he knows of the strange robots, he heads to the docks.
Chapter 3: The Sea and Me
Mario, Luigi, Samus, Wii Fit Trainer, Little Mac, Link, Marth, Bowser, Peach, and Mr. Game and Watch are out on the shore when they come across a massive ship. The massive ship is heading straight towards them, and there are air planes attacking it.
We switch to the ship's perspective, where we find Chibi Robo and Sami defending the ship. Sami manages to shoot one plane down but does not have enough time to shoot the other. The other plane drops a bomb on the ship. As the ship sinks, Sami is shown to have survived and climbs into a lifeboat with only her gun and some supplies.
We switch back to Mario's ship, where Chibi Robo blasts into. They see the planes coming for them when suddenly something under the water passes by. A gigantic purple dragon lifts out of the water underneath Sami's lifeboat, revealing itself to be Ridley. A air wing begins to attack the planes but it is hit on the wing, forcing Fox to eject and land on the ship. They find Kirby who was sleeping in the supply room, stuffed with food.
They see Sami's lifeboat and heads towards it, attacking Ridley from the ship. Ridley becomes agitated and begins to attack them as Sami fires from behind. He destroys the Smash Bros ship, but just then a sword flies through the air, with ninja stars following close behind, shocking Ridley. The sword lands in the hands of Takumaru, and Sami, Link, Mario, Samus, Kirby, and Fox all line up on the wreckage to take out Ridley as he roars.
After defeating Ridley a second time, the Smash Brothers cling onto the wreckage and hope that another ship finds them or that they adrift to a island.
Chapter 4: Champion's Cry
Sukapon goes up for the WWA Championship after beating his robotic bothers. He enters a fighting match against Little Mac and beats him. Just then, Megaman warps in and the two battle. Sukapon manages to take Megaman out and take the championship belt. Sukapon takes the belt, but he then notices a shadowy man disappear just out of the corner of his eye.
Chapter 5: Scuttletown Follies
Mario's group washes up on a island, with a town named Scuttletown just in view.
Donkey Kong, Diddy Kong, and Dixie climb down from trees, with stolen bananas. As they get away, a purple thing hits all three of the Kongs. The purple thing retracts, revealing Shantae. The Kongs and Shantae fight, while King K. Rool enters Scuttletown docks. Shantae and the Kongs stop their fight and team up to take out King K. Rool.
Mario sees the Kongs and Shantae in her monkey form eating bananas and tells them about what Master Hand ordered them to do. The Kongs act in surprise, but then their gaze returns to the bananas.
Chapter 6: The Plains of the Dark Tower
Ness, Shulk, and Ike find themselves under the attack of Slime and surprisingly, aren't doing that well. Just then, Agnes Oblige appears and attacks Slime, catching him off guard. The two fight until a giant heart projectile fires at them, revealing Lucas and his new move PK Love. The six all journey south to a large and dark tower and a distorted crack begins to open up in the sky.