Mega Man Star Force introduces a new lead character, a boy named Subaru Hoshikawa, whose astronaut father has disappeared after a mysterious incident at the satellite station. Fond memories of spending time with his father have inspired Subaru’s interests in the stars and what lies beyond. One day, Subaru heads to the observation deck and puts on a pair of “visualizer” glasses that had belonged to his father. These allow the wearer to see all the electric connections that exist between spaces. When he puts on these special goggles, a specific wave is triggered, summoning the presence of a mysterious alien life form named Warlock who had escaped from the planet FM. Dangerous creatures from that planet have come to attack Earth, so they must join together in order to defeat these menacing forces. Combining with Warlock enables Subaru to transform into Mega Man and enter the Wave Road.

The year is 22XX. Viruses and cyber crime have been eliminated from the net and technology has advanced to an unprecedented level. The world of tomorrow is one where people use mobile computers called "Trancers" and are able to change various navigation systems into electromagnetic waves (EM waves). These EM waves are known as the Wave Road. The Wave Road exists in the real world, however it is only visible to those from the mysterious planet FM and the game’s hero who, through a twist of fate, transforms into EM waves himself.