Disaster strikes when Goemon and Ebisimaru are sent to jail for crimes they didn't commit! After being freed from jail by their female companion Yae, they soon discover that poor-looking phonies are causing mischief under their names! You'll have to put a stop to these impostors to clear your name and save Edo from disaster.

Goemon DS is an action game with RPG elements, similar to the first Nintendo 64 game. Players control Goemon and Ebisimaru, and later gain Yae and Sasuke. As with the N64 game, each character has their own special abilities that allow them to progress through special areas. For example, Goemon earns power gloves that let him push large blocks, while Ebisimaru gets a ballerina dress that allows him to drill underground.

What's particularly eye-catching about Goemon DS, though, is its art style. Similar to Mojib Ribbon, the game looks like it has been drawn on a Japanese scroll with ink. Characters in the game, however, are all polygonal.