After noticing a small amount of evil activity for Team Arch to deal with, and realizing that their lair is in need of repairs from the earthquake that happened in the previous movie, SpongeBob decides to enter Team Arch into the North & South League, a small baseball league for both independent and mainstream baseball teams in North and South America. Team Arch form themselves as the San Francisco Samurais, but they have trouble entering since they don't have State Director. In the rules, each state has to have at least four teams, with all four being led by their respective owners and a State Director. However, they're approached by Richard Sullivan, the California State Director, who's interested to see how they play and invites him to the San Francisco Giants' headquarters, where his office is located. Sullivan realizes their need for payment to fix their lair, and offers them a reasonable contract, which they accept.
While training in Panama, Richard gives them a little warning that they might receive insults from spectators, including racial ones, due to recent events involving a "Cold War" between California and the US Government, who have been at odds with each other because of racial incidents regarding Washington DC residents insulting the multiculturalism in California. While the Samurais are training, and studying about racism due to their small amount of knowledge on the subject, many of the players from the other Californian teams soon sign a petition, stating they refuse to play with the Samurais, but a tragic few of their teammates, along with one of their managers, Len Durham, insist they drop the petition and play alongside the Samurais, but the petitioners relent. The petitioners luck soon changes when the Commissioner of Baseball suspends Durham for actions in his personal life, leaving the Samurai's without a manager to start the league. However, retired Giants player Jack Snow agrees to manage the team.
In their first game, the Samurais take on the Austin Allstars, and experience their first taste of right-wing insults, including some unnecessary judgement from the Allstars' pitcher, Reeves.
In a game against the Philadelphia Blasters, manager Willard Braxton and top player Collin Reynolds constantly taunt Izzy, causing him to mess up most of the time, and go back to the dugout and smash his bat out of frustration. With encouragement from SpongeBob, Izzy then returns to the field. Although he initially ignores Braxton's insults, he gets in the head with beverage cup thrown a spectator claiming that Izzy's being rude, causing Shiro to confront Braxton and Reynolds for their attitude before being sent back. Izzy hits a single, steals second base, and advances to third on a throwing error, and scores the winning run, earning some appreciation from his team and some of the spectators. During an interview, Braxton and Reynolds immediately deny being hard Izzy. The Samurais arrive in Philadelphia for the second game, but are denied entry into any of the hotels for unknown reasons. One of the other Californian players, Walton, tells Team Arch about his passion for baseball and blames them for making the season look bad, resulting in a fight between him and Matt. The news about the Blaster's "racial grip on their home" spreads across the region, and generates bad press for the team. Infuriated by his organization's behavior, the owner requires the players to be respectful from now on and forces Braxton and Reynolds to pose with Team Arch for newspapers and magazine photos as an apology.
In a game against the Pittsburgh Diggers, Diggers pitcher Wellington beanballs Nate in the eye, resulting an unnecessary fight between the two teams. As a result, the Diggers are disqualified and disbanded, much to Team Arch's relief, except for Nate, who thought they won the match incorrectly.
Later, in game against the Cincinnati Bangers, one of the Californian players, Johnston, comes to understand what kind of pressure Team Arch is facing, and makes a public show of solidarity, standing with his arm around Yugi's shoulders before a hostile crowd at Crosley Field in Cincinnati, silencing some and increasing the volume of others.
In a game against the Charleston Berserkers, one Berserker, Samson, "accidentally" spikes Kai on the back of the leg with his cleats while running the bases. Hyoma insists on beaning another Berserker, but Kai persuades him to stay calm and move faster. While recuperating, Sullivan approaches Kai and SpongeBob to tell them that their way of playing reminds him of when he used to play in the Minor League, which is why he recruited them.
For the rest of the season, the Samurais continue to win match after match before finding themselves in the final game of the season against the "country's flagship team", the Richmond Patriots.
In the final inning, Patriots pitcher, Frank Hollier, intent on humiliating the Samurais, throws a fastball at SpongeBob, but with all his might, SpongeBob fiercely hits the ball, sending it out of the park. While the country relents over the Patriots' loss, with their fans mindlessly rioting, Team Arch, their friends and family, and all of California celebrate as SpongeBob scores the winning run, yelling "Somebody call an astronomer, 'cause that ball is out of the park and out of this world!". While the Samurais receive the League trophy, and announce their semi-retirement, Holier tries to protest, but his team immediately takes him away. The movie ends with the team heading home with their trophy.
