The game begins in Mushroom Kingdom, but progresses to Beanbean Kingdom for the majority of the game as Mario and Luigi combat Cackletta, the game's primary antagonist. The quest begins when Cackletta, with the aid of her assistant Fawful, steals Princess Peach's voice after adopting the guise of an ambassador from Beanbean Kingdom.
A role-playing game, it centers on a battle system different from that of traditional games of the genre, with emphasis on timing and more elaborate attacks. The game is whimsical in tone, with various in-game jokes and comical references to the heritage of the Mario series. Superstar Saga was generally well received by critics, and IGN named it the twelfth best Game Boy Advance game of all time in their feature reflecting on the Game Boy Advance's lifespan.