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- The story begins with Mario and Princess Peach on their way to Hyrule castle at the request of Princess Zelda and Link. Along the way, however, they are attacked by Primids, the main army from Subspace. After defeating them, the pair are confronted by a new foe, known as a Blank. This new creature defeats Mario by emitting a beam from his hand very similar to the blast from a Subspace cannon and similarly turns him into a trophy. The Blank takes Mario's trophy and begins to escape, only to be stopped by Link.
The Blank, after relinquishing its prize, turns into a copy of Mario called Nega-Mario. In this new form, the Blank escapes by dropping a small capsule that resembles a Subspace Bomb. This creates a small portal into subspace, which dissapears as sson as it enters. Unnerved by the events, Link takes Peach and the revived Mario back to Hyrule castle. On the way, however, they encounter Serras-Kai and Saki Amamiya along the way, both of whom then attack the group. After the battle, Serras-Kai is turned into a trophy, but Saki manages to escape whith both his fallen friend as well as Link.
- The story skips to Meta Knight and King Dedede, who are searching the rubble of some sort of base when a loud rumble destroys the peace. A large explosion of subspace apears, ripping a hole in space. Emerging from this hole is a massive battleship apears, which then begins to lay waste to the countryside. The two are forced to confront waves of Primids, until they finnally meet up with Donkey Kong and Diddy Kong. The team confronts a massive monster called Allion, which the think they defeat. However, they are surprised by a monster called Kal'ganesh, which lives in Allion's back. The trophies of the warriors are collected and taken into subspace, leaving behind the world.
- Ness, Lucas and Pokemon Trainer find themselves running from the a subspace battleship, witnissing Daisy and Yoshi be taken away by specialized Primids. They escape from the enemies and come face-to-face with another Blank. This one, however, reveals Tabuu's wings are now his. He also inherited Tabuu's Off wave. The Blank commands the Primids to gather the trophies, when Pit and Geno apear and gather the fallen warriors, then dissapear before another Off wave can be used. The two barely escape, boarding a ship that resembles Samus's but of a different color.
- Fox along with Krystal are then seen running through a forest, pursued by Nega versions of Metaknight, Marth, and Wario. As they exit the forest, Fox encounters a horrible, yet somewhat familier, foe; Nega-Rayquaza. They defeat the monster, making them the first ones to actually defeat any of the subspace creatures.
- Meanwhile, Mario and Zelda have arrived at Hyrule castle, only to find a Subspace Battleship floating above it in mid-bombardment. They storm the catsle, finding Nill in the process, and climb the tower up to its tallest point. Nill uses her grappling hook to latch onto the ship, and the three board the ship of Five point, the Suoidisni. They storm the ship and fight with Five point on the Bridge in a vicous battle to the death. After defeating him, he sets a self-destruct sytsem just before he dies. Everyone ecapes without harm.
- This is the first time the player takes control of Saki, Serras-Kai and Geno. The three are in the Comet Observatory, taking orders from Rosalina, who is their leader. They have the several trophies on display, most of which we never saw them capture. The three load into a ship much like Samus', but it is green. They land on another Subspace Battleship, Evalsne. They storm the ship, only to find Allion, however they do not fight it. Instead, they find the trophies of Meta Knight and King Dedede, and begin to escape with them. Suddenly, Right point of the Dark Stars, as well as the first of the Seven Masters to be fought, Betrice. After a long battle, the three heroes escape by knocking right point off of the ship and destroying Betrice.
- The story changes focus to Captain Olimar and R.O.B. who are being persued by a subspace battleship. They run through a castle, finding Lucario as they do so, before finally escaping and confronting Dark Samus, who has alligned herself with the subsspace army. She fights the heroes, taking Marth's trophy for her prize.
- We immediatly see Dark Samus carrying Lucario's trophy, but is confronted by Ike and Roy who defeat her and take Marth's trophy back. The rest of the level is spent running from the Subspace battleship that is after their trophies.
- Waluigi, unaware of all of this, is miles away with Mona and Wario, riding around in a city when Mario and co. run by followed by the subspace army. They leap out of their car and run down the street in an attempt to escape the Blanks. After running for a while, they confront the Subspace Tank, which is dropped from the battleship. After defeating it, they join Mario in his fight against subspace.
- Sonic and Shadow are seen running through a deserted area, the subspace army in hot pursuit. It is at this point that Pikachu is finally introduced, also running form Blanks. The three come across a portal to subspace, from which Nega-Daisy emerges. They defeat her and enter subspace, finding Daisy's trophy in the process. When they escape subspace, they encounter Epsinoron of the Seven Masters. Upon defeating him, they escape to find Captain Olimar and R.O.B..
- Kirby makes his late apearance at this point, alongside Snake and Sora. The three are seen in a base of some kind, trying to find Samus. After they dig deep into the base, they do ultimately find Samus, as well as Dark Samus. Upon defeating Dark samus, the group begins their escape, stopped only by Ridley. After defeating him, they load onto Captain Falcon's Falcon Flyer and make their escape. They spot Mario and his now rather sizable group, and set down next to him.
- Ike, Marth and Roy are taking on another subspace battleship, the Reqnoc. They storm the ship alone and defeat High Point of the Dark Stars. While escaping they rescue Fox and Falco. After the ship crashes, the exit it to find that Mario and co. have gathered at the crash site.
- Ike reasons that if they leave someone trophy unnatended, as a bait. The plan works better than they supposed, and they have to stop Blanks from taking it. Against Geno's better judgement, Serras-Kai decides to set down and gather up the trophy, but is confronted by Mario. The player chooses who they want to play as, and then fight. Regardless of who wins, Mario, Pit, and Kai escaped from overwhelming amounts of Primids and Blanks by getting in Kai's ship and escaping back to the Comet Observatory.
- Meanwhile, Nill takes command of the group left over (much to the dismay of Wario and Waluigi) and a group of four goes to get the subspace battleship running while another group of four goes to get the other battleship that crashed. The first group finds Ike and his group, while the second finds Sonic's group, completeing the party.
- At this point, the other characters available in Super smash Bros. Crisis may be unlocked, with the exception of Felicia, Morrigan, Monkey D. Luffy, Travis Touchdown, Chich & Kino, Cire, megaman and Bass.
- The group gathers at Mario's location, the Comet observatory, and begins to formulate a plan. The player chooses two teams which will take of the last two cubspace battleships while the captured two destroy the last one. The remaining characters will be on a ground assault on the main subspace portal, and can be selected later.
- The first group takes on the subspace battleship Yortsed, which is captained by Left point. Before they fight him (or Thetanion) they take on Allion once again. They defeat him and Kal'ganesh, but it still stands back up. The heros have no power to take on the creature, but the creature realizes that the last attack destroyed the collar that kept him bound by the blanks. Allion then turns on the blanks and destroys the ship.