The Mages are lead by Heishin, with Seto as his right hand man. Other authoritative figures include the 5 High Mages, Secmeton, Anubisius, Atenza, Martis, Kepura, located in various Shrines. Each High Mage is served by another lower ranking mage at the Shrine.
After long searching Heishin acquires the Millennium Rod. Using it he begins to plot getting the other Millennium Items, in order to fulfill the pact of acquiring great power, by bringing them together at the Forbidden Ruins.
Hesihin first attacks the King and Queen's palace in search of one of the Items. Simon Muran badly beaten slips the Prince Atem the Millennium Puzzle, hoping he could escape with it. Heishin meets Atem and after defeating him in a Duel demands the Puzzle, but Simon encourages the prince to shatter the Puzzle. Doing so Atem and the Puzzle both disappear.
In Atem's absence the Mages acquire the remaining Items bar the Puzzle and begin to govern the land. The Millennium Eye, Ring, Key, Scale and Necklace are given to the High Mages, who guarded them at their Shrines.
After Atem's return Seto betrays Heishin and helps Atem acquire the Items off the High Mages and uses him to find the Forbidden Ruins. He then leads Atem to Heishin. After Atem defeats Heishin, Seto leads Atem to the Forbidden Ruins, where he reveals his plan, that he had used Atem to gather the Items, so he could use them to acquire the power himself. Atem defeats Seto in a duel reclaiming the Items, but Heishin appears and holds a knife to Seto's neck demanding the Items. Atem hands them over and Heishin uses them to Summon DarkNite. According to the pact Heishin says that DarkNite is to obey him. DarkNite claiming to have made no pact with the likes of him turns Heishin into a card and destroys it.
After Atem defeats DarkNite, the Mages lose all power they once had. Atem then governs the Kingdom as potentate.