When Mystique visits College Station, TX pretending to be TMR on a surprise visit home, Mayor Berry is kidnapped and held hostage by a league of super-villains. The villains, led by Magneto and Dr. Doom, tell TMR that the only way to retrieve the Mayor is to defeat them all in a fantasy baseball league.
TMR is distraught and confides in the Say Nay Kid, who says that there is nothing they can do and all hope is lost. TMR refuses to give up and is able to enlist the help of his 10 top awesome superheroes (minus Space Ghost and adding Deadpool, much to the horror of 5 year old TMR). Thanks to a screw-up by Pod Vader, Aquaman is also contacted and offers to help, but nobody wanted the help of freaking Aquaman.
TMR accepts the villain's challenge, and is put into a 12 team mixed league against Magneto, Dr. Doom, Green Goblin, Lex Luthor, and others. While the draft is taking place, Professor X and Iron Man are busy trying to find the villain's hideout, which is discovered to be a heavily fortified Castle Doom.
As the weeks progress and the heroes try to find a way into the castle, the chances of winning are looking bleaker for TMR, as he has been hit by the injury bug. However, he does not realize how much the villains would not want to lose to each other, as they have refused any kind of collusion with each other. They have also become distracted by the thought of actually winning at something. As the heroes move closer, TMR slowly climbs the league standings and barely makes the playoffs in the last week of the season.
TMR's good luck persists, as he makes his way to the league championship game to face Dr. Doom. The heroes finally infiltrate the castle on the last day of the league. However, Albert Pujols (who had led TMR's team for the entire season) is suddenly attacked by Lex Luthor's henchmen as he heads to the stadium on the last day. Nobody thinks he will be able to play, but TMR is unable to edit his lineup to remove Pujols because Magneto has scrambled all internet connectivity in TMR's radius.
The inhuman Pujols still manages to play, and TMR manages to eek out a victory after a walk off grand slam by Pujols. As this is happening, the heroes manage to win a devastating fight against the villains, saving Mayor Berry at the last second.
As the movie ends, Albert Pujols is seen walking toward the hot tub. He takes off a mask and reveals himself to be Aquaman, who wanted to prove that he was not the worthless super-hero that everybody believed him to be.