Technology has improved substantially since the events of Battle Network. The world is now connected via a network of EM Waves powered by three colossal satellites orbiting the planet. Normally invisible to humans, Geo Stelar can see the EM Wave World thanks to a device called the Visualizer. With the help of a friendly FM-ian named Omega-Xis—and a device called a Transer—Geo must explore the EM Wave World as Mega Man and rescue the humans from those FM-ians who have come in search of the Andromeda Key. Along the way, Geo discovers the fate that befell his late father—and the reasons he had for creating the BrotherBand that Geo eventually relies upon.
Mega Man Star Force 2 continues the story two months after the original, introducing new characters and destinations, along with a powerful device called the OOPArt. The third and final entry in the series brings Geo far afield before ultimately returning him to his home where his quest to learn about his father meets its conclusion.