The last world that the fighters travel to is our world(which happens to be the world of Miis). There they meet a man named Shigeru Miiyamoto, who, after hearing of their plight, agrees to help them find the rest of the fighters.
When the all the fighters are rescued, they agree to leave our world since no one in our world has any powers. They are lust about to leave when Tabuu's entire army attacks Mii world. Tabuu had planned on the fighters rescuing each other and simply waited until they were all in one place before unleashing an Off Wave to turn all the fighters(with the exception of Miiyamoto) into trophies, causing Bowser Jr. to drop the Smash Ball given to him earlier by the Crazy Hand. Tabuu's forces then carry the trophies to The Shake King's and Dr. Eggman's ships.
Miiyamoto know that without the fighters, Tabuu can't be stopped. He spots the Smash Ball Bowser Jr. dropped and picks it up. It dissolves into his hand and imbues him with his normal moveset and his smash attacks. He first proceeds to The Shake King's ship to rescue the first half of the fighters and defeat The Shake King.
After defeating The Shake King, he travels to Eggman's ship to rescue the other half of the fighters and defeat Dr. Eggman, who is piloting the new Egg Smasher. Once this is done, the fighters agree that as long as Tabuu is using Shadow Lugia to boost his powers, he can't be defeated. So they agree to free Shadow Lugia, who goes berserk after being freed as a result of being used. Forcing a boss battle between him and the Pokemon Trainers.
Miiyamoto must defeat Tabuu himself. After Tabuu is defeated, the portals linking their location in subspace to other locations in time. to disappear. The lives of the four Marios, the three Links, The Prince and Vectorman are now in jeopardy, as Baby Mario, Young Link, The Prince and Vectorman can no longer return to their individual time lines. Lugia, who has now been purified as a result of the battle, tells Mewtwo and Deoxys that if the three of them combine their psychic powers, they may be able to contact Celebi and have Celebi return the time-shifted fighters to their own time lines. This turns out to be a success as all the fighters are returned to their homes in their own time lines, on their own home worlds and in their own dimensions. The credits feature cutscenes of the fighters settling back into their old lives. The Crazy Hand, Bowser and Bowser Jr. helping the Master Hand recover and readjust to being in Smash World. And R.O.B. building a new home, happy to at last be reunited with other members of his own kind.