Professor Thelonious Viper, known in Japan as Professor Cobra「プロフェッサー・コブラ」(Purofessā Kobura), is a professor hailing from West Academy.
While performing military services in a war-ravaged country, Viper came upon an infant who he believed saved his life by drawing his attention away from an area which was suddenly detonated. In the English dub it simply stated that the rest of the unit he was with was ambushed and captured while he left them. He adopted the child, Pierce, and came to regard him as the "angel" in his otherwise torturous life. Years later, chasing after Duel Monsters cards given to him by Viper as a present that were swept up in the wind, Pierce was run over by an oncoming vehicle (the dubbed version of that scene is cut, here, he died of an illness).
Later on, Viper enters Duel Academy in the third year and in a desperate attempt to aid Yubel, who promised to raise his son from the dead, Professor Viper pits students against one another in Survival Duels. The only concern he has is that Adrian Gecko grew suspicious of him. Viper attempted to get rid of him by forcing him to into Survival Duels and setting the bio band drainage level to maximum in an attempt to kill him knowing that Adrian would still duel, but Adrian forced Viper to lower the level when he got the entire Ra and Obelisk dorms to duel at the same time. When Jaden Yuki and his friends break into Viper's hideout, Viper finds that Yubel still needs more energy and faces off against Jaden in a duel (in the English version, part of the reason was that Yubel wanted to see Jaden suffer). When he loses, Yubel, disappointed that Jaden has not suffered sufficiently, appears as an avatar of energy in the shape of his son. Before disposing of him, it mimics Pierce's voice, adding insult to injury by saying that Viper failed him prior to "disposing" of him. (Cobra's death is different in the Japanese version: Yubel, manifesting in energy form as Cobra's son, instead re-writes Cobra's memories of Rick's death, tricking him into believing that Rick never died. In a stupor, Cobra follows his "son" to the edge of the platform where he seemingly falls to his death. All of this was cut from the US version: after Yubel grabs Viper's face, he simply disappears, which heavily implies his death though this is not specifically stated. Footage was taken from the beginning of the following episode to cover the time otherwise noticeably large cuts.)
Viper is seen one more time prior to Jaden's duel with Yubel, as Jaden remembers all the people Yubel has wronged.