A comet brings the end of the world, and two kids realize their only weapon is to stop fighting separately, Netto and his NetNavi have to become one thing to survive it. The show strips away the collection-game comfort of earlier Rockman.EXE and forces a genuinely apocalyptic stakes question: what does it cost to fuse with your AI partner when the alternative is extinction? Cross Fusion isn't a power-up anymore. It's the only prayer you have left.

A comet streaks across the sky, and with it comes catastrophe. Massive digital viruses begin manifesting in the real world, destroying everything they touch. Netto and Enzan use cross fusion to step in, but they are swept off to an unknown place, where they meet the one behind the attack: Duo. Picking up right where Rockman.EXE Axess ended, after the fight with Dr. Regal and Nebula, this third Rockman.EXE series pits Netto and Rockman against a mysterious net navi from space whose mission is to wipe out planets steeped in darkness. Because of the evil spread by Regal's Dark Chips, Duo has marked Earth for destruction, and Netto and Rockman must try to show him that the planet holds real good.