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According to Higsby, the Professor was a high-ranking WWW member. He had a great deal of respect of Wily's dream and even made it his own as well. When Wily was supposedly killed at the end of Mega Man Battle Network, the Professor decided to take matters into his own hands and attempt to start the war that Wily wanted.
Needing funds to do so, he began by bringing Zero out of storage from the Zero Account and spread his virus across the Net via StarMan.EXE's phony vaccine. By the time Lan and MegaMan had faced Zero in combat, the Professor had already gathered enough money and recreated the Life Virus. From there, the Professor declared his intentions to the world and began to prepare the Life Virus.
Undaunted, Lan, MegaMan and their friends made their way to the WWW Space and destroyed the Life Virus. The Professor was unafraid despite this, due to the secrecy of his location and that he could simply start anew. However, Zero had used his virus, which had been the Professor's computers for some time, to inform the NetPolice of his location, and the Professor was hauled off to jail.
The Professor appears in Rockman.EXE Beast+. He announces his existence and that he is responsible for the data plant and beast viruses that have been spontaneously materializing around the world, which have been seen in the first few episodes. He is also responsible for the creation of the Zero Virus, which was used to materialize beast viruses in the real world; the result of his research on the remains of the Super Cybeast. It is revealed that the Professor was using the data plant to absorb electricity from power plants and other sources to use for the revival of the Super Cybeast.
Unlike his game counterpart, Yahoot reveals that the Professor was a WWW researcher who was not seen in the field like members such as himself. The Professor was also a fanatic about Dr. Wily's ideals and quit WWW after Dr. Wily disappeared, stating that there is no point to WWW if there is no Dr. Wily. He later became an independent researcher and contacted Yahoot a while ago.
It turns out that he owns a Sushi Factory and has his research laboratory located directly underneath it. His laboratory was unveiled when Lan, Dex, and Maylu fell down the shaft leading to it to escape the sushi-making robots.
His intentions became clear when CF-MegaMan discovered a giant stasis chamber that was rebuilding the Super Cybeast. Afterwards, the Professor was cornered by CF-MegaMan and CF-ProtoMan, but escaped after the Super Cybeast went berserk and escaped onto the net.
Like his game counterpart, he treats Zero as a mere pawn and tool that only exists to serve him. After Zero had enough of his arrogance, he left the Professor and disappeared. Appalled by Zero's actions, he later created Zero One, a duplicate without any emotional data.
The Professor resurfaced several episodes controlling a giant Sushi-shaped airship. He then used Zero One to attack the NetPolice HQ. The airship was destroyed when Zero sacrificed himself to destroy the airship by transporting the highly-damaged Zero One near the airship. (Zero One was programmed to self-detonate upon deletion by the Professor). He escaped by parachute and was promptly arrested by the NetPolice.