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Having grown tired of the dreary scenery in the Underworld, Hades decides to make the Magic Kingdom his new summer home; however, Merlin would be able to easily repel an invasion with the power of his magic crystal. In an attempt to outwit Merlin, Hades sends Pain and Panic to steal the crystal, however their bumbling leads to the crystal being shattered into eight pieces that scatter to each area of the Magic Kingdom. Merlin recruits the player to help him find the pieces of his crystal, giving them magical cards with the Sorcerer's Crest on them; the crest itself is used when specifically needed.
Needing help himself, Hades revives Ursula, Maleficent, Scar and Dr. Facilier, promising them second lives in exchange for a crystal fragment. The two witches have schemes of their own to usurp power. Posing as Boss Teal - Underworld Crime Boss, Lord Indigo of the East Underworld Trading company and Lazuli, god of the underworld, Hades also promises Cruella, Ratcliffe and Yzma something they each want in exchange for help; the 99 puppies, Pocahontas' land, and to be empress of Adventureland respectively. Under the alias "Prince Azure", Hades also forces genie Jafar into helping. Though he meant to guide the player throughout the kingdom, Merlin forced to fight off Hades' lesser pawns that are trying to invade. Therefore, the player's guidance comes from a foe of each villain: Sebastian, Merryweather, Rafiki, Mama Odie, Pongo, Pocahontas, Kuzco, and Genie.
When all the villains are defeated, the magic crystal is restored. However, Hades isn't one to give up; he sends in Chernabog - his "Number 1 Guy". Unfortunately, it was only a distraction to let Pain and Panic try stealing the crystal again; they predictably fail. Deciding to use brute force, Hades amasses his army of the dead, which is led by the other villains. Through Merlin's guidance, the player uses the magic of the Sorcerer's Crest to seal Hades and the villains inside the mystic crystal. The crystal is then returned to Merlin's study. Inside the crystal, Hades is left to wonder what went wrong with his plans.