At the beginning of the film, we are introduced to Halloween Town, an alternate world where the annual holiday of Halloween is constructed, and to its biggest celebrity, Jack Skellington, the Pumpkin King. Although Jack is loved and respected by the townspeople, he has become bored with the repetitiveness of Halloween and feels that there is something missing from his life. While wandering in the woods after one such Halloween, with his loyal ghost dog, Zero, Jack discovers a circle of trees he has never seen before, a nexus to several holiday-themed worlds. Each tree has a door on it with different icons from the holiday seasons, such as a four leaf clover or a heart, but Jack is immediately attracted to the door in the shape of a Christmas tree. When Jack opens this Christmas tree door, he is sucked into a town filled with snow, lights, and happiness. Jack is mesmerized by all the colors and cheerfulness, and realizes that this may be what he has been searching for.
Upon his return to Halloween Town, Jack immediately calls for a town meeting. During the meeting he reveals several of the artifacts he brought with him from Christmas town. Unfortunately, the denizens of Halloween Town only think in terms of how these toys could be used for Halloween. Frustrated from the misunderstandings, Jack describes the ruler of Christmas Town in the only way the town members can understand: as a lobster-red creature possessing a deep voice and riding his sleigh "like a vulture in the sky," his name, "Sandy Claws". Distraught by his friends' inability to understand Christmas, Jack locks himself in his house and performs multiple experiments to try to understand the meaning of Christmas. He finally comes to the realization that believing in Christmas is all it takes and he informs the town of his intention to take over Christmas for that year. Jack then assigns each of the townspeople certain duties in order to make Christmas theirs, including having Sally sew Jack a Santa Claus outfit and having Dr. Finkelstein bring several skeleton reindeer to life. In order to complete this takeover, Jack enlists the help of a trio of young trick or treaters named Shock, Lock, and Barrel to "Kidnap the Sandy Claws." After mistakenly kidnapping the Easter bunny the trio bring Santa Claus to Jack, who tells them not to take Santa to Oogie Boogie - but they end up doing so anyway. Despite Jack's efforts to make their Christmas joyful, the townspeople end up mixing the ideas of Christmas and Halloween, creating twisted toys and decorations.
Sally, who is secretly in love with Jack, has a vision about the disasters to come and tries to warn him that taking over something he knows nothing about may be a bad idea. However, Jack is too wrapped in his fantasies to listen, so she attempts to stop Jack's departure by creating a fog bank; but Zero's lighted, jack-o-lantern nose allows Jack to see.
Now Christmas eve, Jack embarks from Halloween Town to share Halloween Town's toys with the whole world. Unfortunately, the citizens of the real world are not so receptive to these Halloween-themed toys and begin to call police reporting attacks from toys and a "flying skeleton." Soon after, the military is called in to deal with the Santa Claus imposter, eventually shooting Jack out of the sky. At the same time, Sally sets off to rescue Santa Claus in order to set things right. However, during her rescue attempt she is also captured by Oogie Boogie who perversely gambles with both of their lives. The other citizens of Halloweentown witness Jack being shot down, and, fearing the worst, begin to mourn his death.
Meanwhile, the citizens of the real world are being informed that since the real Santa Claus can't be found Christmas must be cancelled. Upon regaining consciousness in a graveyard amongst the wreckage of his failed Christmas, Jack hears this news and realizes his foolishness. He realizes that his role in life is to be the Pumpkin King and vows to make the next Halloween the best ever. In an effort to save this Christmas, Jack returns to Halloween Town to save Santa Claus. He rushes to Oogie's lair to rescue both Sally and Santa Claus and in defeating Oogie reveals him to be nothing more than a sack full of bugs. Santa Claus informs Jack that he can easily save Christmas, after all he is Santa Claus, and magically floats out the chimney and restores peace to the real world by replacing all of Jack's presents. Jack returns to Halloween Town to the great joy of its citizens and Santa is seen flying over Halloween Town wishing the citizens a Happy Halloween while Jack responds with a Merry Christmas. With him, however, Santa brings snow and the citizens of Halloweentown finally understand the Christmas spirit.
Finally, Sally reveals her true feelings for Jack. The movie ends with Jack and Sally embracing and giving each other a kiss. Zero flies into the sky and turns into a star.
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