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The story mode in Super Smash Bros. Rebirth is called " The Puppetmaster's Tricks" and features the Hands and Puppeter Bowser as the anatagonists.
Chapter 1: A Reuniting Fight! Puppeter Bowser Approaches!
It's been a couple years since the last Smash tournament, and the Smashers have met back up. During the reunion party, the villains attack, thus starting off the next Smash tournament (FIGHT: Any starter characters vs. Bowser, Ganondorf, Wolf, Master Hand, and Crazy Hand). After the fight, Bowser introduces his latest creation - Puppeter Bowser! Master and Crazy Hands succumbed to the power of Puppeter Bowser and have become it's "hands". Just as Ganondorf is about to command Puppeter Bowser to attack, the entity breaks free of it's magic chains and sends every Smasher (including the villains) into different worlds.
Mario and Villager wake up in Dream Land, which is being overrun by Giygas' army under the control of Puppeter Bowser. The two arm themselves and get ready to fight their way through (EXPLORATION: Green Greens - Mario and Villager - 3 Lives). They arrive at the Halberd to find the Masked Man and Meta Knight working on a way to get out of Dream Land and back into the World of Trophies.
The quartet of heroes heads off into the skies of Dream Land, but not before encountering one of Puppeter Bowser's Doomships. Mario leaps off the Halberd to head through the Father-Doomship.