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 forgetting about him afterwards (they died in the shipwreck in the Japanese 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 his Dark Duel Disk (In the Japanese version he found the remains of his siblings there instead, confirming that his family had died in the shipwreck).
Rafael's main cards are the Guardian cards he kept with him during his time on the island. He dueled Yami Yugi, and gave him the Orichalcos Card, and Yami 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 Yami's soul, but got Yugi's soul instead. Yami 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's soulless body, and entered Dartz's temple, where Dartz revealed to him that he was the one responsible for the typhoon. Rafael attempted to use the Seal of the Orichalcos on Dartz, but it backfired and took Rafael's soul.
He was released when Dartz and the Orichalcos God were defeated.