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In the intro of the game, the player is introduced to the world of toons , which looks the same as Earth. The player is then transported to the mid-air stadium, where there's a full house. The player is then intorduced to Minnie Mouse and Haruhi Suziyama who are egerally awaiting a battle. The audience then cheers, as two cannons shoot out two shadowy figures. The first one is of Spongebob Squarepants, and the second one is of Mickey Mouse. The two toons get ready to fight. (Battle: Spongebob/Mickey Mouse) Depending on who the player chose either Mickey or Spongebob will win. Meanwhile, unbeknowest to the toons above, Bluto and Peg-Leg Pete are secretly hiding out in a plane with weapons, and strange creatures. Back in the Stadium, Spongebob and Mickey shake hands to the joy of Haruhi, Minnie, and the audience. Then, the sky turns completely black and Pete and Bluto jump out of the plane with their weapons. Mickey decides to fight Pete, but Pete shoots out a blast of darkness and sends Mickey flying. Spongebob decides to avenge Mickey, but Bluto knocks him out cold. Bluto and Pete then kidnap the girls, and fly off. They leave some enemies as well as a darkness bomb to distract Spongebob. Spongebob wakes up just in time to fight off the enemies. (Fight darkness minions: Spongebob) Spongebob finishes off the enemies, and looks at the bomb. The bomb shows 10 seconds left. Spongebob jumps out of the stadium just in time, as the stadium in engulfed in darkness. Spongebob looks around and is angered to find out that both Bluto and Pete have disappeared. with the girls/\. He then decides to run back to Bikini Bottom and get help.
The story then moves to the Island of Sodor. A blue tank engine by the name of Thomas is pulling a passenger train, and everything is going well. King Koopa is hiding up above with the same weapons as Bluto and Pete. He shoots a blast from the cannon, and the matter forms a train robber. Koopa orders the newly-created robber to attack the train, and the robber obeys. The robber jumps on top of Thomas' cab, and makes a loud thump on the cab. Thomas and his crew notice that something's up, and his driver decides to investigate. The driver tries to fight the robber, but it punches him off the train. The fireman tries to fight him as well, but ends up like the driver. The robber drives Thomas off much faster than before. The driver picks up his cell phone and calls Sir Topham Hatt. Sir Topham Hatt gets the message, and runs to Tidmouth Sheds. He fetches Percy, and drives him to the hijacker. Finally they catch up to the runaway train. Sir Topham Hatt jumps off of Percy, and on board Thomas. The robber is shocked to find out that Sir Topham Hatt is standing there. It grows larger, and jumps on top of the train. Sir Topham Hatt follows. (VS Train Robber: Sir Topham Hatt) Sir Topham Hatt defeats the robber, and is shocked to see that the robber wasn't even real! He then looks up, to where the matter flying up. King Koopa laughs and jumps into his Doomship, while Sir Topham Hatt follows him on foot.
Spongebob runs back into Bikini Bottom, only to find out that he was beat by the Knights of Darkness who are being led by Man-Ray, and the Dirty Bubble. The knights are destroying downtown Bikini Bottom. Knowing that he can't defeat them on his own, he begins to look for his friends. On the way to the Krusty Krab, however he is stopped by none other than Plankton inside of a giant robot. Plankton knocks down all of the buildings around Spongebob so that he can't escape. A battle ensures, and Plankton defeats Spongebob, and turns him into a trophy. However, in King Neptune's castle, a mermaid princess is watching the battle and the defeat. Determined to save Bikini Bottom and her friends, Mindy leaves the castle to fight the Knights of Darkness.
- "What the heck is wrong with you guys?" - Authur Read speaking to both Peter Griffin and Ernie the Giant Chicken