The story takes place in the challenge mode of the game. Mario and friends travel to Baseball Kingdom for some relaxation and to play some baseball, when Bowser Jr. suddenly appears and throws the island into chaos. Mario must travel around the island and through each of the unique and specialized areas in order to recruit different characters and captains to challenge Bowser Jr. to a game of baseball. Once Bowser Jr. has been defeated, he retreats, but then Bowser appears to challenge Mario's team and take over the island. Upon defeating Bowser, Mario's team all celebrate and throw a huge party. Bowser and Jr. are invited to the party as well and Bowser ends up saving Mario from one of Wario's and Waluigi's tricks.