In the Ketchup Kingdom, a hare-like boy named DeMille is an outcast because he doesn't like tomatoes. Disliking tomatoes in the Ketchup Kingdom is illegal, and the punishment for such people (referred to as "Droppers") is being locked up until they do like tomatoes. DeMille's girlfriend, Patharan, also hates tomatoes, and she is kidnapped by King Abīra, leader of the Ketchup Kingdom. DeMille must go on a journey to save Patharan.
Tomato Adventure is an action-command RPG. The player battles enemies when they bump into him on the screen. Battles are fought using Gimmicks, toy-like weapons. Using Gimmicks, the player must play a mini-game correctly in order to hit an enemy. Types of Gimmicks include Time, which require timing, Speed, which requires the player to finish a task before time runs out, Excite, which covers miscellaneous games, and Input, which requires the player to press buttons or enter information in a certain order. If the player fails a mini-game, they have to start all over.