The story of Major League Baseball 2K9 revolves around creating and managing your own baseball team through the franchise mode. This involves playing entire seasons with hundreds of matches, as well as handling managerial tasks like studying statistics and hiring players. The goal is to balance team performance while meeting the desires of your star players.
The game also includes various multiplayer modes, such as training, Home Run Derby, and Postseason mode, which can be played against other teams or solo. Players can unlock special items, like training cards, to enhance their gameplay experience.