Master Evil first appeared as a shadow vortex with a sinister face, punishing both Fusion Mask and Syndy Chross for failing him after their loss to Team ZEXAL. Next, Team ZEXAL reached the final Web Point, in the Duel Stadium, which was guarded by Master Evil. Kaito asked him why he was doing that, and he explained that he took part in the Duel Team Carnival once, but was banished from it because his team was too strong and their opponents would just run away - because of that, he planned to wipe the Duel Team Carnival from existence. Then, the stadium's door shut, and Master Evil challenged Team ZEXAL to a Duel, saying that should they lose, the stadium would collapse and they would be crushed with it, making the tournament never be held again. Yuma then Dueled him.
During the Duel, it was revealed that Master Evil observed Team ZEXAL Dueling the Obots, so he developed a strategy to counter Yuma's moves. At one point, when Master Evil had cornered Yuma and kept claiming that he was the strongest Duelist, Mr. Heartland appeared from a screen and explained that Master Evil was actually banned because he was found cheating many times in the tournament, and that his grudge comes from being found out and barred from participating in the tournament. Yuma, however, manages a comeback and defeats Master Evil.
After being defeated, Master Evil is arrested. As he is escorted, Yuma thanks him for the fun Duel, saying that he was a strong opponent. Master Evil smiles, and says to himself that the Duel was indeed fun.