It takes place a few months after MegaMan NT Warrior. SciLab is trying to find a way to create Cross Fusion but are unsuccessful. Then a dimensional area generator appears and traps SciLab in a Dimensional Area. ShadeMan.EXE and BeastMan.EXE steal the Synchro Chips, but the two remain and Lan Cross Fuses with MegaMan.EXE to fight off BeastMan.EXE. He becomes a NetSavior and fights to get rid of the Dark Chips and Nebula. Lan and MegaMan are initially the only ones who can Cross Fuse, but later Chaud Blaze and ProtoMan.EXE gain the ability to Cross Fuse too.