A visit by Dahlia Brinkley, the only Springfield Elementary graduate ever to enter an Ivy League college, gives Lisa a severe inferiority complex because she is involved in very few extracurricular activities. When Ned Flanders resigns as coach of Bart's Little League team, the Springfield Isotots, Lisa seizes the chance to extend her résumé and takes the position. Since she knows nothing about baseball, she seeks advice from the patrons of Moe's Tavern, who direct her to Professor Frink and his scientific colleagues. She learns about sabermetrics from them and uses this science to organize the Isotots' strategy; as a result, their record quickly improves and they rise in the league standings. However, Bart eventually rebels against her management, saying that she has taken all the fun out of the game, and hits a home run despite her orders to let the pitcher walk him. The Isotots win the game, but Lisa throws Bart off the team for his insubordination.
The dismissal raises tension at the Simpson household, with Homer and Marge siding with Lisa and Bart, respectively. Homer believes that Lisa needs to do what is good to the team, while Marge thinks she should reconsider, since the family comes first. Under Lisa's leadership, the team advances to the championship against Capital City. On the day of the game, Marge takes Bart to an amusement park; while they ride the roller coaster, Lisa calls Bart to beg for his help, but he brushes her off. Mike Scioscia, manager of the Los Angeles Angels of Anaheim, pops up in the seats behind Marge and Bart and tells him that the best players listen to their managers, pointing out his three World Series wins — two as player, one as manager. Marge takes Bart to the game, which is now in its last inning with the Isotots down 11-10. Bart puts aside his differences with Lisa and offers to pinch-run from first base, then ignores her signs and steals both second and third. As he begins to steal home, Lisa realizes the odds are vastly against him, then decides to ignore the numbers and cheer him on anyway. He is tagged out at the plate, costing the Isotots their championship bid, but Lisa thanks him for helping her learn to love baseball as a game, and the team cheers them for resolving their differences.