When Lan wakes up and realizes that his battle with BeastMan and his CrossFusion with MegaMan weren't just a dream, he rushes to SciLab, which is still in shambles from the battle. Lan ends up walking off with a SynchroChip, and it's a good thing he does--ShadeMan starts deleting NetCity, and after MegaMan is unable to stop him, viruses start appearing in the Human World! It's up to Lan and MegaMan to CrossFuse and stop them, but ShadeMan still manages to come out on top. Using the data he stole from NetCity, he fashions a powerful fortress. From there, he plans to strike out at the Human World and drive everyone off the planet!