Chaud schickt ProtoMan ins Zentrale Computersystem, um MegaMan wiederherzustellen. Glücklicherweise gelingt dies. Gemeinsam greifen die beiden PharaohMan an und schwächen ihn so, dass Mr. Wily ihn leicht gefangen nehmen kann. Doch PharaohMan will nicht für Sterbliche arbeiten und greift zu verzweifelten Mitteln.
The BlasterMan/StoneMan clones attack PharaohMan, but he escapes unscathed. Roll and the others are not so lucky and are turned to stone by PharaohMan. As this part of the Cyber Net begins to collapse, ProtoMan succeeds in saving MegaMan's frame. SharkMan, SkullMan, and WoodMan work at shutting down SciLab's main computer, while ProtoMan takes on PharaohMan single-handedly. Just when it seems ProtoMan will be deleted, MegaMan returns and the two NetNavis attack PharaohMan with the Double Program Advance. BlasterMan and StoneMan reappear and take the weakened PharaohMan to Mr. Wily at World Three Headquarters. MegaMan follows them but is immediately set upon by BlasterMan and StoneMan, so Lan engages MegaMan's new ability, StyleChange, which allows MegaMan to easily defeat the Solo NetNavis. In the end, Mr. Wily and PharaohMan's showdown of wills ends in the destruction of World Three Headquarters.
ボンバーマン・ストーンマン軍団がファラオマンを包囲、攻撃するが無傷のファラオマン。その場に居合せたロール達もファラオマンによって石化させられてしまう。辺りが崩壊する中、ロックマンのフレームを救うブルース。ブルースは単身ファラオマンに戦いを挑むが、危機に瀕したブルースを救ったのは復活したロックマンだった。二人はダブルプログラムアドバンスでファラオマンを攻撃。さらにスタイルチェンジしたロックマンがストーンマン・ボンバーマンを攻撃する。
PharaohMan invia un satellite verso Dentech City, e nessuno sembra essere in grado di fermarlo. Tuttavia, all'ultimo momento, MegaMan si rigenera e, assistito da ProtoMan riesce a sconfiggere PharaohMan grazie ad un doppio programma avanzato, riprendendo così il controllo della rete. Utilizzando poi una nuova abilità chiamata Style Change, MegaMan si trasforma e riesce a fermare Stoneman e BlasterMan prima che prendano ciò che resta di PharaohMan e lo consegnino nelle mani di Mister While, il capo della Mondo Tre.
