Geo Stelar is having a hard time adjusting to life after his father vanished in a space station accident three months ago, and it does not help when a group of children from his class try to forcefully make him attend school again. However, Geo's life takes a startling turn when he witnesses a battle between two EM waves one night, one of which collides with him in a flashy beam of light.

Tom returns to AMAKEN after weeks of absence, but he is completely under Cygnus's control now. He attempts to throw Aaron off a skyscraper, but Mega Man rescues him. After a heated battle with Cygnus Wing, Tom reveals to Geo that Omega-Xis was the one who killed Kelvin. The startling news causes Geo to collapse into a river where he is washed away.