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。
The Bombman and Stoneman army attempt to capture Pharaohman and force him into working for the World Three, but they're easily deleted. The original Bombman and Stoneman versions escape, while Pharaohman turns Roll, Glyde, and Iceman into stone. Meanwhile, the net agents' Net Navis (Sharkman, Skullman, and Woodman) attempt to hack into the science lab's programming to locate Pharaohman, and do so... just in time to get turned to stone as well. Everyone soon learns that Pharaohman is sending a satellite to earth, with it's crash-landing destination to be Densan City! Hope is scarce... until Blues rescues Rockman's body from a pool of hot magma, and goes to face Pharaohman himself. Blues faces deletion, until... Rockman is revived and appears to help! Using a double Beta Sword, they force Pharaohman to log-out! Rockman follows him to the World Three network, where he takes on Bombman and Stoneman by himself. Using a new Style Change technique, Rockman easily defeats them both.
