Many, many years after the events of Megaman Battle Network, the world has changed. Net navis still exist, but they are no longer part of the daily life of everyone in the world. PETs have been replaced by a device called a "Transer". A transer has all of the same functions of a PET, but it deletes viruses also without the need of a net navi. Networks no longer exist. They have been replace by EM Waves. Three sattelites help keep stability in the world. Leo - Pegasus - Dragon. However, there is still evil at work. EM Waves called FMs are creatures that can merge with humans for nefarious reasons. Their goal - destroy Earth, like they destroyed the AM planet. However, unknown to them, 4 AMs survived the attack. One of which has stolen something from them and is on the run... Enter Warrock (Omega-Xis)

Subaru Hokishiwa (Geo Stellar) is a quiet, lonely, but normal boy. His father was a EM Wave researcher who died in the crash of a satellite. Ever since, he has been quiet and lonely. He doesn't go to school, he learns at home, and enjoys staring at the stars, wondering about his father... One day, as Subaru is using his visualizer, given to him by his father, to watch the EM waves, a war between two EM waves break out with Subaru caught between in between...