Lan and MegaMan are the Net's only hope now that Dr. Regal has unleashed the ultimate manifestation of Dark Power, an entity known as Nebula Grey, that threatens to delete them forever.
Megaman and Lan Hikari go deeper into the UnderNet and meet PharoahMan from a ancient civilization, who has four warriors that are each as powerful as MegaMan, but MegaMan is determined to defeat them and become the strongest NetNavi in DenTech City.
Transformed by the mysterious "beast" program, MegaMan has developed the unwelcome power to turn into a rampaging monster. Lan's scientist dad searches for a solution while MegaMan and Lan try to deal with MegaMan's beastly new condition.
Lan Hikari and his NetNavi MegaMan continue to get stronger, but when they achieve PerfectSynchro, MegaMan flips out, and the NetPolice must destroy him before he destroys the world.
Lan and MegaMan must defend DenTech City against Bass, a juvenile delinquent who can mimic any foe's power and who is responsible for putting Lan and MegaMan on the top of the most wanted list in DenTech City.
Lan and MegaMan are on the run. Even with the help of BubbleMan, they can't escape the long arm of the law now that they've become DenTech City's public enemy number #1.