Entrance to Subspace
The level starts with the player fighting average enemies, beginning with an ambush against Floows and Boom Primids. After this, the stage auto-scrolls and the player has to avoid Metal Primids, Boom Primids, Primids, Spaaks, and Borborases; then, the level stops for the player to fight another ambush. This time, the player has to stop the Subspace Generators from spawning Fire Primids. Metal Primids, and Borborases; the player then goes on a big straight path. By this point of the level, only ambushes remain, in order of an Armank, a Greap and Big Primids, and finally an Armank with Big Primids. At the end of the level, there is a section of invisible platform. The final (and only) door of the level isn't golden, which is unusual.
In a cutscene, Bowser and Ganondorf are seen walking in an unknown area of Subspace. Ganondorf pulls out a Dark Cannon and fires at his former ally, who falls as a trophy, and kicks him aside. Ganondorf then calls forth Master Hand, who appears before him. Ganondorf bows, but then sees that Master Hand is being controlled by the Chains of Light. He looks up further to see Tabuu, who had manipulated him the whole time. Infuriated, Ganondorf leaps up to attack Tabuu, who brings up a shield to send Ganondorf flying back downwards. Ganondorf becomes a trophy upon impact with the back of Master Hand. This action, however, releases Master Hand from the Chains of Light, and he forms a fist to fly towards Tabuu. This attack is also easily deflected with Tabuu's shield, and Master Hand falls to the ground.
All the other characters suddenly appear, ready to fight. However, Tabuu goes into his winged form and releases his Off Waves, which turn all of the characters into trophies. Tabuu then pulls together the pieces of the World of Trophies that were pulled into Subspace by the Subspace Bombs, and forms them into The Great Maze.
After completing The Subspace Bomb Factory (Part II), all the smashers that had joined the player's team will merge into one group so the player(s) is no longer required to select a group when replaying previous levels. This also gives the player(s) a variety of characters to choose from in this stage. Since Tabuu turns everyone into a trophy, everyone is lost afterwards.
List of enemies