The Subspace Bomb Factory (Part II)
The stage opens with Donkey Kong, Diddy Kong, Captain Falcon, and Olimar entering the island after they defeat the Subspace foes from a previous level. After the level, they show up to confront the Ancient Minister, with Samus and Pikachu already in the room from the previous level. The room is full of Subspace bombs, lined up with R.O.B.s. The heroes are ready to fight the Minister, but he doesn't seem to fight. Seeing that the Minister is not following orders, a hologram of Ganondorf shows up to take control of the R.O.B. Squad. The R.O.B.'s begin to advance towards a bunch of Subspace Bombs, but the Minister stops them. Angered, Ganondorf pushes a button to stop the R.O.B.'s from obeying the Minister, and their eyes started glowing red. As they begin to take the Bombs down, the Minister knocks them away, but Ganondorf overrides their free choice and forces them to attack the Minister. He is bombarded with lasers and eventually catches fire. Ganondorf laughs and disappears as a flock of Auroros enter to distract the heroes. However, the Minister fires at them and destroys them, showing that he's still alive. His robe and armor flies off in all directions to reveal the Master R.O.B. After this, the player may choose from the aforementioned characters to ward off the enemy horde.
After defeating the enemies, the gang starts to try fighting off the R.O.B.'s who are trying to detonate Subspace Bombs. R.O.B is in melancholia, and pays no attention to Diddy's screams for help. Realizing there's not enough time, Captain Falcon calls in the Falcon Flyer so they can all escape from certain doom. DK carries the miserable R.O.B to safety, and they leap down a shaft. As they descend towards a pit, the Falcon Flyer pulls up beneath them, catching them and shooting down a tunnel towards safety. As they rush through the tunnel, however, Meta Ridley notices them and gives chase, desperate for revenge against Pikachu and Samus, starting a boss battle that the player must clear within two minutes to pass.
Back on the Canyon, Mario spots the big explosion, along with Link, Pit, Yoshi, Kirby, Marth, Ike, Ice Climbers, Pokémon Trainer, and Lucas, who all recently teamed up to fight off the massive ambush of the Subspace Army. Soon, the Falcon Flyer and the Halberd carrying Meta Knight, Lucario, Snake, Peach, Zelda, Fox, Falco and Mr. Game & Watch lands, and all the fighters are united.
After The Subspace Bomb Factory II is completed, the Falcon Flyer escaped from the destroyed Isle of the Ancients and landed on the ground, along with the Halberd, where Mario, Pit, Kirby, Link, Yoshi, Marth, Ike, Lucas, Pokémon Trainer and Ice Climbers looked the explosion of the Isle of the Ancients, provocating a big reunion of all the characters, except Luigi, Ness and King Dedede, forgotten on the cave, where was the explosion that consumed King Dedede's castle, Wario, also forgotten but in the path to the ruins, where was sucked by Galleom's explosion, and Bowser and Ganondorf, the high-ranking villains, all them join all the heroes in the Subspace, being saved by them.
Plus second group, piloting the Halberd
And plus third group, piloting the Falcon Flyer
List of enemies