Seeing the destruction of the world in the future, Primo returns to the past in an attempt to destroy New Domino City to prevent the disaster from ever occurring. He later becomes obsessed with defeating the player after they are chosen by god's will to fix the future as well as defeating him in a Duel.
Primo first appeared alongside Jakob and Lester where the three of them witnessed the destruction of the world. They later teleported back to their throne room where Jakob stated that the destruction of the world was inevitable to which Primo responds that was the reason as to why they returned.
To the Future - State of the WRGP and the World
Primo later appeared after the player and their team had defeated Team Catastrophe, sending the Diablo onto the Duel Lanes in an attempt to kill them. After this failed, he approached the player, questioning why they received a Blank card from the gods, calling it a fluke of their will. He then transforms into his alternate form and challenges the player to a Duel, also informing them that the Diablo are currently Dueling their friends and will destroy them. After the player has defeated Primo, the damage from the Duel causes him to explode.
Upon winning the Duels in the World Racing Grand Prix, the player, along with Yusei and Jack find out that they were against Team New World. Primo first went up against Yusei, where he questioned where the player was. Yusei told him that he'd have to get through him first, which Primo laughed at, stating that it'd be nothing but a warm up. Utilizing his Meklord Emperor Wisel, Primo easily defeated Yusei and later Jack, even absorbing Jack's "Red Nova Dragon" in the process. The player then Dueled Primo, but upon entering the track, their blank cards reveal themselves, surprising Primo, which the player later used to defeat him. He then returned to the pit, where Lester showed amusement at his loss, which angered Primo.
After Jakob is defeated by the player, he teleports them to a room to discuss how they have shown them that maybe the future can be changed by the hands of mankind and not god's will. The three of them then disappear. Primo can later be challenged to a Duel on a computer, located in the Memorial Circuit waiting room.