After defeating everyone in the Medabot tournament, wait until the credits end. You will see someone robbing your trophy. After the short intermission, the Rubberobo Gang will can be challenged at the normal places you usually battle (Forest, Factory, etc.). Although you cannot defeat them completely, you can get Medaparts.

After you beat all the challengers in the tournament, the Rubberobo Gang will steal your prize. You will then get to fight various Rubberobo members at all locations on the map. There are certain areas on the map that contain the four Rubberobo Captains (Squidguts, Gillgirl, Shrimplips, and Seaslug). You will fact them in that order. Seaslug uses the Ultimate Medabot, Mega-Emperor. Mega-Emperor is has extremely high firepower and armor. Make sure you have a very strong team.