The plot (as told by Challenge Mode) is that the main cast has gotten into playing baseball recently, including Bowser, who challenges the main characters to face his team. Mario, Peach, Yoshi, Donkey Kong, and Wario accept this challenge and form their own teams, all itching to prove to the others and Bowser that they're the best baseball team around.
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Mario Superstar Baseball provides examples of:
- The Computer Is a Cheating Bastard: During the harder levels.
- Instant-Win Condition: The Mercy rule is on by default, automatically ending the game if one team has a 10-run lead by the end of an inning. If you beat another team this way in Challenge Mode, you'll instantly recruit every single member of that team that you haven't already.
- Interface Spoiler: The characters that make up Bowser's team are visible on the list of characters you've recruited in Challenge Mode, even though it's not possible to recruit them, giving away that Bowser will get his own story mode. Speaking of Bowser's story, it's not possible to recruit any of the other captains because all of them join Mario's team for the final game.
- Mini-Game: There's 7 minigames, one for each stadium plus Toy Field:
- Mario Stadium: "Bob-omb Derby", a home-run derby with firework-loaded Bob-ombs instead of baseballs.
- Peach Garden: "Wall Ball", where four players pitch the ball to try and break a line of walls for coins.
- Yoshi Park: "Piranha Panic", in which four players have to throw colored eggs and Bob-ombs at the matching Piranha Plants (or, with Bob-ombs, each other).
- Wario Palace: "Chain Chomp Sprint", where the players run around the bases collecting gems and must stop or be penalized when the sleeping Chain Chomp in the center wakes up.
- Donkey Kong Jungle: "Barrel Batter", a puzzle game where a lone player tries to break clusters of colored barrels by hitting the ball at them.
- Bowser Castle: "Star Dash", where four players run around collecting coins and helpful powerups while dodging Thwomps.
- Toy Field is a Mario Party-esque turn-based game where the players bat, pitch, and field (who does what depends on how each turn plays out) on a special field to earn coins.
- Petal Power: Daisy's Star Skill covers the ball with flowers.
- Playing with Fire: Both Mario and Luigi's Star Skills engulf the ball in flames.
- Power Fist: Donkey Kong uses a boxing glove to hit the baseball.
- The Power of Love: Peach's Star Skill obscures the ball with hearts.
- Ship Tease: Mario has good chemistry with Peach, while Luigi has good chemistry with Daisy.
- Villain Episode: Completing Challenge Mode with Mario, Peach, Yoshi, Donkey Kong, and Wario unlocks Bowser's story, where he seeks out the other teams himself since no one responds to his challenge. After defeating every team, Bowser comes back home to find that Mario hijacked his stadium, leading to a final match against Mario's team, which is now made up entirely of captains.
- We Cannot Go On Without You: Non-Game Over variant that isn't applied to the player. If you recruit the main captain of an opposing team in Challenge Mode, you can't challenge that team anymore. Any players left over will find their way onto Bowser Jr.'s team to give you a chance at them again.