With Ciel's Resistance he defeated Copy X, the ruler of Neo Arcadia. The terror of the Neo Arcadian regime ended, but the energy shortage remained a constant problem. Ciel devoted herself to researching new forms of energy. And Elpizo became the newly appointed Resistance leader. However, overcome by his desire for power, Elpizo awakened the Dark Elf, whose magic had once nearly destroyed the world. Elpizo, thirsting for the power of the Dark Elf, lost sight of his true duty, and was finally defeated after a fierce battle. However, the Dark Elf fled, her destination unknown... The battle over the Dark Elf had only just begun.

Two months after the events of Mega Man Zero 2, a spaceship that crashed only recently emits energy similar to the Dark Elf. Zero, Ciel and a pair of Resistance members set out to investigate. Not long into the mission Ciel and the two Resistance members are captured by Neo Arcadia as Zero enters the ship. However, they are not harmed, nor are they held prisoner, as an incident breaks out involving a giant Reploid named Omega that not even Leviathan and Fefnir combined can handle. Zero interrupts the battle and is left to handle things on his own. Soon thereafter Dr. Weil is introduced, with a seemingly ressurected Copy X in tow, who then reclaims leadership of Neo Arcadia, much to the chagrin of Harpuia.