Two hundred years have passed since the Battle Network series, and the PET has transformed into the Transer (which later is superceded by the Star Carrier). These new forms of PETs no longer carry Navis, but they can utilize Navi Cards and do just about everything else that PETs used to accomplish.
Seeking out extraterrestrial life, the government agency NAZA set up a space station called “Peace” and attempted to make contact with alien beings. They succeeded in opening communications with a world known as FM; however, unfortunately the FM king mistook their contact as a threat of war, and he decided to make a preemptive strike against these humans from Earth. He assaulted the space station, rendering it out of commission, and then prepared to attack Earth itself.
A man named Kelvin Stelar was one of those who was on Peace, and he disappeared when the people of Earth lost contact with the space station. Crushed by the loss of the father he loved and admired so much, his son Geo pined away at home, refusing to go to school or to have interaction with just about anyone as he spent his hours staring at the stars.
But all of that changed one day when an alien landed in his Transer.
Omega-Xis, one of the few remaining AM-ians, is an energy-based being from another planet. He escaped his doomed planet just before it was destroyed by the FM king (who attacked AM for the same reason he attacked Earth). In an attempt to stop the FM-ians, Omega pretended to be one of them, and through his deceit, he managed to steal the key to their superweapon Andromeda. He promptly fled from the FM-ians and ended up hiding out in Geo’s Transer.
Since AM-ians and FM-ians are both wave-based creatures, they discover they can morph with the humans on Earth and grant those humans the ability to travel on the electronic “Wave Road” which is invisible to the normal human eye. The FM-ians that arrive on Earth in pursuit of Omega take advantage of this to possess some of the humans they come into contact with and use them toward their own ends.
In order to counter the FM-ians, Omega uses heavy-handed tactics to convince Geo to fuse with him and help him fight his battles. To keep this a secret from others, Geo adopts the hastily-assumed name of “MegaMan” for when he is in morphed form.
Through the course of their struggles against the FM-ians, Geo and Omega gradually learn to work together, and together they discover the value of friendship. Omega finds himself softening around the edges and even decides to stay with Geo after the FM king is defeated and Andromeda is destroyed. Geo slowly opens up and begins to make friends, some of whom even learn of his secret identity.
The story of the battle against the FM-ians and the destruction of Andromeda is told in Star Force 1.
Even after the FM-ians are defeated, the world is not at rest. Once, in the past, a tribe of people known only as “Mu” possessed the secrets of the Wave World and knew how to manipulate EM waves to great effect. A scientist in the present studied that empire and now wishes to unlock their secrets, planning to take over the world using its EM waves.
New friends and new foes (and a few who are both at the same time) are introduced in Mega Man Star Force 2.
A descendant of Mu, named Solo, possesses the ability to Wave Change without the necessity of morphing with an EM being. He calls his wave form “Rogue” and feels that no one should command the power of the Mu, save for himself, as the last descendant of that empire. This, however, doesn’t stop Omega-Xis from eating the Out of Place Artifact and acquiring some of the power of one of the lost tribes of Mu.
For more information on this and other plot points, check out the various game hint pages for details about the story that this history lacks.