Players: Red Pianta, Blue Pianta, Yellow Pianta, Blue Noki, Green Noki, Red Noki, Monty Mole, Blooper
Captain: Princess Peach
Sub-Captain: Princess Daisy
Sub-Captain: Bowser Jr.
Team Donkey Kong
Captain: Donkey Kong
Sub-Captain: Diddy Kong
Mario and Luigi are enjoying a normal day in their house, when they receive a ransom note from Bowser, stating that he's kidnapped Peach and taken the Baseball Crystals, and the only way to get her back and retrieve the crystals is to beat him in a game of baseball. Mario and Luigi quickly scramble across the Mushroom Kingdom, gathering any baseball players they can find. They can gather any characters on the Mario, Yoshi, Donkey Kong, Wario, and Paper Teams. Players from Peach's team can also be gathered, though their captain, Peach, cannot. Only until Bowser is beaten will Peach join the team. Once she is freed, they all celebrate, and the crystals will form a rainbow. Players from Bowser and the Koopalings' teams can be gathered by going to Bowser's Castle, and challenging each of the players.
Once every player that is not on team Nintendo is obtained, the characters can travel back to Bowser's Castle and find a room where Bowser had been working on a machine that can allow players to pass through alternate dimensions. If the player has purchased the appropriate parts from E. Gadd's Lab, they can complete the machine, and travel to places in alternate universes, including Dream Land, the Temple of Time, Corneria, Brinstar, Pallet Town, Onet, Castle Siege, Mist Flow, and Emerald Hill Zone. In these various places, a hero of the same series can be brought back to play baseball.
Team Square Enix
Once you think you've completed the story by unlocking team Nintendo, the game has one more surprise. The Star Ship will fly down and the Square Enix characters will take over the stadiums. The player must go to all of the stadiums and defeat the Square Enix characters who have taken over them. Once you've beaten all of them, Ninja will propose a 9-inning game, and Star Pitches and Star Swings are turned off. You're gonna be playing a fair game of baseball, so GOOD LUCK! AND LET'S PLLLLAY BAAAALL!
Ending/Final Boss Battle
After you defeat Ninja, the Baseball Crystals will form into a big multicolored crystal on the Star Ship and everyone will go home and celebrate, that is, if they are playing on Normal or Hard difficulty levels. If they are playing on Expert or higher, the crystals will combine into a big, dark crystal that will envelop the ship into darkness and teleport it to another dimension (the characters get ejected from the ship). The other dimension, at the ruins of what appears to be a baseball stadium (the diamond is still there) is revealed, and the crystal materializes into Bahamut, who appears on-screen with a header that reads "Dragon King Bahamut from Final Fantasy" (the Final Fantasy logo is in place of the words Final Fantasy, though.) You have to beat Bahamut as the final boss battle.