A proud warrior of the FM Planet, Omega-Xis, betrays his kind and escapes to Earth where he makes contact with Geo Stelar. Like his fellow extraterrestrials called FM-ians, Omega-Xis is capable of initiating a process known as "Electromagnetic Wave Change," which transforms ordinary humans of the same frequency as themselves into "EM Wave Humans," allowing them to freely operate in the EM Wave World. With these new powers, Geo becomes known as Mega Man, a hero of Echo Ridge. However, Omega-Xis holds the key to accessing the weapon Andromeda, capable of destroying planets. As such, many FM-ians pursue Omega-Xis with the intent of retrieving the key in their goal to destroy the Earth. Meanwhile, Omega-Xis also knows the secret to the disappearance of Geo's father in a catastrophic space accident months ago.

The second series follows the events of the second game focusing on the lost continent of Mu. The ancient civilization vanished ages ago, and a few of its remnants still exist as myths and legends called UMAs (Unidentified Mystery Animals similar to FM-ians that also have the ability to fuse with humans).