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Arrathir Quinn, a young Magic player goes on the search for a card shop that supposedly sells Alpha (the first Magic set ever printed) boosters. He wanders into the YGO-verse by way of a rip in the fabric of the Multiverse and meets Yūgi and Jōnouchi.
They create a blended version of the Magic and Duel Monsters rules and Arrathir duels Yūgi and Kaiba, beating them both.
Afterwards, Arrathir and Yūgi meet Khell Dracos, a summoner from Dominaria. Yami no Marik returns and Khell teaches Arrathir how to summon.
Kaiba launches a second Battle City tournament. Arrathir and Khell enter and both make it to the finals. It is also revealed Pegasus has created a new Egyptian God card, Anubis, God of Death. Yami no Marik steals the God card for himself.
The finals are held in the virtual world, but hackers attack the KaibaCorp mainframe, trapping the finalists in the virtual world. They battle their way out, only to face the real mastermind behind the attack: a sentient AI program designed by the hackers. They defeat the program and continue with the tournament.
Arrathir ends up against Yami no Marik in the semifinals. He is crushed by Anubis' attack and dies.
He wakes up in the graveyard and a strange man named Gurth brings him before Lu Chao, a powerful Planeswalker who reveals the story of the Keepers of Mana and that Arrathir is the reincarnation of Chikuro, the Keeper of Black Mana. (The Keeper's name isn't revealed until partway through The Awakening. Before this, he is referred to as "The other Arrathir".)
Arrathir is reborn, but with the spirit in control. He defeats Yami no Marik and is set to duel Yuugi in the finals. Khell confronts the spirit who knocks him out.
Partway through the duel, the spirit reveals his true self. As he is about to land the killing blow on Yami no Yūgi, Arrathir takes control on their body, begging Yami no Yūgi to attack him. When Arrathir looses, he awakens in his Soul Room and meets the spirit, who kicks the crap out of him.
A few days later, Khell leaves for Dominaria and Arrathir returns home the next day.