In Mega Man Star Force: Red Joker, players travel between the physical world and the digital world via electromagnetic waves that form wave roads. Geo Stelar, the protagonist of the game, can see these wave roads through usage of his unique visualiser tool. Once in the digital world, Geo can merge with the electronic life-form known as Omega-Xis to become Mega Man. The wave roads are being overrun by mysterious noise, generated by an approaching gigantic meteor that threatens both the physical and digital worlds of MMSF3. Fortunately, Mega Man discovers that he can control the Noise, using the new Noise Change system to transform into Red Joker form...

Players with friends who own Mega Man Star Force: Black Ace can share unique items and powers utilizing the Nintendo Wi-Fi connection, enhancing their individual characters.