Lans Dad schickt die NetNavis der fünf Freunde ins Wissenschaftslabor, um MegaMans Frame zu holen. Dort wird GutsMan von PharaoMan gelöscht. Doch auch die StoneMan/ BlasterMan-Armee ist zur Stelle, um PharaoMan gefangen zu nehmen. Ein Kampf ist unausweichlich.
Lan's dad, Dr. Hikari, has devised a way to rebuild MegaMan! Now that the gang has assembled MegaMan's data, it simply has to be input into MegaMan's cyber structure, or ""Frame,"" and rebooted. Unfortunately, this Frame is located inside SciLab's computer network, which is now under the control of PharaohMan. It's going to require a tremendous team effort, a crazy cyberdog, and a lot of Mrs. Hikari's spaghetti to hack into SciLab's maximum security system! Meanwhile, the secret Net Agents Commander Beef, Black Rose (Sal), and Mysteriyu (Miyu) have enlisted Higsby's help to find a back door to the Cyber Net so they can hack in, shut down SciLab, and capture PharaohMan. But they're not the only ones after the fearsome pharaoh! BlasterMan and StoneMan return with an army of clones on a Wily mission of their own!!
帰国した熱斗の父・裕一朗は、ロックマンを蘇らせることができるという。そのためには科学省のメインシステム内奥底にあるロックマンのフレームが必要である。ファラオマンが支配する科学省に乗りこむ熱斗たち。科学省の電脳空間はファラオマンの影響により砂漠化していた。プラグインしたロール・ガッツマン・アイスマン・グライドは、ロックマンを復活できるのか？
Al fine di far rivivere MegaMan, la sua struttura di back-up deve essere recuperata dalla rete dello Sci-Lab. Tuttavia, PharaohMan ha preso il controllo di tutta la rete e l'ha trasformata in un deserto. Il padre di Lan ha un piano per recuperare la struttura di MegaMan, ma occorre che i Net-Navi degli amici di Lan si introducano nello Sci-Lab; PharaohMan interviene e costringe tutti alla fuga
