Dr. Light has developed Litanium, a rare material that Dr. Wily has learned about and wants for himself to create a powerful Plasma Blaster. After Mega Man repels Wily's forces, Wily tries formulating another plan to take the Litanium when a portal opens inside Skull Fortress. Now, Mega Man and X must team up to defeat the evil alliance of Dr. Wily and Vile before the Reploids can return to the future with the Litanium.