Beams of light are tearing through cities all over the world, deconstructing anything they touch into network data. Dr. Hikari recognizes this as the dreaded "Spectrum" program, and he commands Lan to quickly rush and destroy something called the "Tadashi Hikari" program. As MegaMan rushes to do so, Bass assaults him, but Colonel intervenes. The destruction of the program is interrupted when a large beast named Nebula Grey appears and absorbs it, causing the NetNavis to retreat. Just then, the Spectrum beams tear through an amusement park, deconstructing many of Lan's friends. Dr. Regal reappears, having transformed into a data being after his demise with LaserMan in Axess, and plans to extract the programming written on Dr. Hikari's retinal pattern, completing Spectrum and transforming the planet into network data. Lan, Chaud, and Raika work together to infiltrate a Netopian army base where Dr. Regal goes through with his plan, and Lan encounters a man named Baryl who claims to be Colonel's NetOp. MegaMan jacks-in to the core of the program to stop Regal, and Bass also appears. In a pinch, MegaMan sacrifices his Ultimate Program to Bass, hoping he can defeat Nebula Grey with it. The resulting fusion creates BassCross MegaMan, a being that obliterates Nebula Grey and spoils Regal's plan. The military base begins to crumble, and Bass absorbs Nebula Grey's power for himself. The NetSavers and Dr. Hikari escape, but Baryl remains behind, uttering the reassuring claim that he is "immortal." Everything deconstructed by Spectrum returns to normal, and peace is restored.
