Medabots: Rokusho is the companion title to MedaBots: Metabee. The player assumes the role of Ikki Tenryou, a boy who loves Medabots. When he is talked into buying a Medabot instead of dinner, Ikki discovers it is missing a vital medal. When a mysterious man named Phantom Renegade gives his father a medal, Ikki can finally compete against other Medafighters in Robattles. However, an organization known as the Medamaniacs are stealing medals and Medaparts from kids. Ikki must track down the source of the trouble.

Medabots can be built and customized using Medaparts. If a player wins a battle they get a Medapart, but if they lose, they must give up one of their Medaparts. In battle, turns are taken based on a Medabot's speed and how long it takes to get to the center of the battlefield, and after each turn they run back to the edge. Each Medapart has a defense rating, with damage depending on this. When a Medapart is destroyed, the Medabot can no longer use this Medapart to attack. When a Medabot's head is destroyed, the other Medabot wins.

Storyline and gameplay are identical between Metabee and Rokusho, but there are version-exclusive Medabots and Medaparts.