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Growing up, Rafael had a perfect life with a wealthy and loving family, but one day while they were on a cruise, it entered a typhoon caused by Dartz (though Rafael did not know this), and he was separated from his family, with them dying in the shipwreck (they forgot about him in the 4Kids version), and he became trapped on a deserted island. As he tried to find a city, which was merely an illusion, he was pulled underwater by Dartz, whom he joined up with. He then went to a graveyard and found the remains of his siblings there instead, confirming that his family had died in the shipwreck (found his Dark Duel Disk in the 4Kids version).
Rafael's main cards are the Guardian cards he kept with him during his time on the island. He dueled Dark Yugi, and gave him the Orichalcos Card, and Atem was "forced" to use it to win (even though no souls were at stake). Because of this, however, Rafael won, and the Orichalcos tried to take Atem's soul, but got Yugi's soul instead. Atem dueled Rafael in a rematch and defeated him, but as the Orichalcos tried to take his soul, he overcame its power. However, as the building collapsed, Rafael fell over the edge.
He survived the fall while carrying Mai Kujaku's soulless body, and entered Dartz's temple, where his boss revealed to him that he was the one responsible for the typhoon. Rafael attempted to use the Barrier of the Orichalcos on Dartz, but it backfired and took his soul instead.
He was released when Dartz and the Orichalcos God were defeated.