During the war, Alister's younger brother Mikey was kidnapped by Dartz (disguised as Gozaburo), and he joined Dartz from here (unaware that it was he and not Gozaburo who wronged him). His main target was Seto Kaiba, as he hated him because of what he thought Gozaburo did (despite the fact that Kaiba, though he is quite mean sometimes, is not like Gozaburo and had nothing to do with any crimes he committed). He disguised himself as Pegasus and dueled Kaiba, and soon revealed his true identity. The theme of his deck was fire. He used the Seal of Orichalcos so that the loser of the duel would lose their soul, but both their life points went down to zero, and neither duelist lost their soul.
Alister had his rematch with Kaiba on a plane, using an army deck, but Kaiba defeated him, and the Orichalcos took his soul. From where he was, however, he heard Dartz say that he was the true kidnapper of his brother. He was released when the Great Leviathan was defeated, and continued searching for Mikey.
He later had a cameo appearance in Season 5 while Pegasus was talking.