A year after the film, Jack Skellington once again feels Halloween has become dull and repetitive. He talks with Dr. Finkelstein improving the next Halloween with new scares and discoveries. The doctor gives Jack the "Soul Robber", a green, whip-like weapon. He then leaves to look for new frights; remembering his lesson from before, Jack searches solely in his world. Equally bored Lock, Shock, and Barrel revive Oogie Boogie, who brainwashes Dr. Finkelstein into creating minions for him. Oogie also kidnaps five of the seven Holiday World leaders. Oogie plans to become the "Seven-Holidays King" once he takes control of Christmas Town. But on December 23, Sally manages to send a magical paper airplane to find Jack to warn him of what has happened.
Jack returns to Halloween Town on Christmas Eve, just to find Oogie's shadow. After defeating the shadow, he is given the Halloween Holiday Door and finds everyone was deceived by Oogie into boobytrapping the town.
Jack learns Sally is imprisoned in a crypt, fighting through Oogie's minions to the graveyard. Once in the crypt, he finds Sally when a giant spider clings her to the ceiling and attacks Jack. Jack defeats the spider, saves Sally and receives the Valentine's Holiday Door. When Jack and Sally walk out of the crypt, she gives Jack an idea to use his Pumpkin King powers to defeat Oogie's monsters.
Sally then says she's worried about Dr. Finklestein and Jack goes to find him. Inside the doctor's lab, Jack finds the brainwashed doctor, who attacks him. Jack returns the doctor to normal by switching his brain back. Jack then goes to the Mayor's courtyard to save the Vampire Brothers. Each vampire gives Jack a key to the mayor's house. Jack finds the mayor and stops Lock, Shock, and Barrel; however, they drop him into a huge maze filled with booby traps. Jack escapes the maze and asks the mayor to release the holiday leaders.
Jack soon realizes Oogie wants to kill Santa, and travels to Christmas Town. Jack rescues Santa from a train-contraption, but Oogie, having become enraged by Jack constantly foiling his plans, leaves in Santa's sleigh full of Christmas presents. Luckily, Sally brings Jack's sleigh to help, and Jack and Santa chase after Oogie. Oogie falls out of the sleigh into a world of garbage after being frightened by one of Jack's jack-in-the-boxes that was dropped in the sleigh by an elf. There, he absorbs the waste and insects in the environment in a fit of rage and becomes a giant version of himself to beat Jack. Jack faces Oogie one-on-one. Oogie spills out his bugs, becoming nothing more than an empty husk, ending his threat for good. Afterward, Jack apologizes to Santa for almost ruining Christmas again, but having a change of heart about the skeleton, Santa thanks him for saving his life.
Afterwards, Jack realizes that his home and loved ones are something more important than new discoveries. The story ends in much the same way as the film does, with Jack and Sally embracing on top of Spiral Hill.