The Ultimate God is located at the bottom of the Aerial Fortress Seibal, and is sleeping since ancient times. In the past, rituals were conducted between Duel Priests, in order to combat and seal this being, who people feared. It is said that should a Duel Priestess lose the ritual Duel, the Ultimate God shall awaken. It also appears that in order to keep this God sealed, not only the Duel Priestess must win, but she should also be offered as a sacrifice for the God.
In the thirtieth century B.C., Rex and Roman became Duel Priests and conducted the Festival of Duality attempting to revive this God who was said to be able to realize any wish - they wanted to revive Ish Kiq Goodwin, the previous Duel Priestess who was sacrificed for the ritual. For that purpose, they convinced the Duel Priestess from that time to lose on purpose, which caused the sun to hide and a disaster to happen, killing many people. Rex and Roman then headed towards the Aerial Fortress Seibal in order to reach the God; however, Rex was completely dominated by its colossal dark miasma, causing him to go crazy.
In the present, Rex and Roman use Sect Ijuin and Akiza Izinski as the Duel Priests to conduct the Ritual Duel once more in an attempt to revive the Ultimate God. For that purpose, Goodwin always planned on Akiza's defeat.
After Akiza loses the ritual Duel, the Ultimate God opens its eyes. With Sect's victory, he becomes the King of Earth's Lock. Rex, Roman, Yusei and Jack then conduct Duels inside Seibal in order to decide the King of Sky's Lock, who would conduct a Duel against the King of Earth's Lock which may open the Ultimate God's door and set him free.
Finally, Yusei becomes the King of Sky's Lock, and Duels against Sect. Meanwhile, the defeated Duel Priestess, Akiza, is offered as a sacrifice, with the Ultimate God slowly draining her life. In the beginning of the final ritual Duel, the Ultimate God starts its resurrection, and produces a roar which thrills Yusei and Jack due to its power.
Once Yusei frees Sect from the miasma of his Duel Dragon and brings him back to his old self, Yusei and Sect plan on a way to seal the Ultimate God for good. Sect reminds about the Skeleton Knight explaining to him about the "Light Sense", which shall seal the Ultimate God. As Yusei and Sect deliver the final blow of the Duel, with the Ultimate God ready to revive, they create the "Cross Sense Final Section" - the "Light Sense" which eradicates the Ultimate God's massive miasma and puts him back to sleep, freeing Akiza.
However Rex Goodwin reveals he holds part of the God's shadow miasma within him and that despite it being sealed the Ultimate God can still be revived. Goodwin chants an ancient language that both Akiza and Yusei recognize as Diak in order to absorb the remaining shadow miasma from the Ultimate God. After doing so Goodwin takes out a blank card and proceeds to absorb the energy from the duelists and the cards they own from both the Aerial Fortress Seibal and the Duel Gate in order to restore the Ultimate God Ultimaya Tzolkin card to normal. Goodwin reveals that all Duel Monster cards including the Duel Dragons originated from the Ultimate God itself.
When Rex Goodwin summons "Ultimate God Ultimaya Tzolk'in" in his Duel with Yusei, the Ultimate God awakens and breaks free from his seal. Then it transforms into its true form: a gigantic red dragon while being under Goodwin's control.