Young urban professionals Jesse McLaughlin (Arye Gross) and his girlfriend Kate (Lar Park Lincoln) move into an old mansion that has been in Jesse's family for generations. They are soon joined by Jesse's goofy friend Charlie Coriell (Jonathan Stark), who brought along his diva girlfriend Lana (Amy Yasbeck), in the hopes of being discovered by Kate, who works for a record company.
Jesse has returned to the old family mansion after his parents were murdered when he was a baby. While going through old things in the basement, Jesse finds a picture of his great-great-grandfather (and namesake) in front of an Aztec temple holding a crystal skull with sapphires in the eyes. In the background is a man Jesse learns is Slim Reeser, a former partner of his great-great-grandfather turned bitter enemy after a disagreement over who would get to keep the skull.
Reasoning that the skull must be buried with him, Jesse and Charlie decide to dig up Jesse's great-great-grandfather in the hopes of procuring the skull. They unearth the casket only to be attacked by the corpse (Royal Dano), who then shows himself to be friendly when Jesse reveals his identity as the senior Jesse's great-great-grandson. Jesse and Charlie take the cowboy zombie, nicknamed "Gramps", back to the house, where he is horrified to learn that the skull has not rejuvenated his body as he had hoped.
Gramps and Charlie go out drinking and driving, and later the boys listen for hours to Gramps' stories of the Old West and his outlaw life. Gramps explains that the house was built using stones from the Aztec temple, and that its rooms act as a hidden doorway across space and time, with the skull acting as a key. He charges Charlie and Jesse with defending the skull against the forces of evil, who are drawn to possess the skull.
During an impromptu Halloween party thrown by Charlie, Gramps makes an appearance (though he is overlooked as it is a costume party), Kate leaves Jesse (taking Lana with her) after he is seen with an old girlfriend by her smarmy boss John Statman (Bill Maher), and Jesse and Charlie pick up two new pets in the Jurassic era, a baby pterodactyl and a caterpillar-dog that's dubbed a Cater-Puppy, after a barbarian/caveman arrives at the party and steals the skull.
Bill Towner (John Ratzenberger), an electrician and "part-time adventurer", arrives to inspect the house's old wiring. While seemingly a buffoon, he pulls a short-sword from his tool case and leads the boys through "one of those time-portal things...you see these all the time in these old houses." In the mystic past, the three fight off a group of Aztec warriors and rescue an Aztec virgin who was about to be sacrificed.
Eventually, a zombified Slim Reeser makes his appearance. Still after the skull, Slim shoots Gramps who then gives Jesse his guns and reveals that it was Slim who shot and killed Jesse's parents when he was a baby. Jesse jumps through a window into the Old West, and eventually succeeds in killing Slim by blasting off his head with a rifle shotgun. Gramps, who has been mortally wounded, begins to pass away. Gramps says goodbye to Jesse and tells him he is so happy to have met his great-great-grandson. Gramps then gives a final warning about the power of the skull, encouraging Jesse to get what he wants from the enchanted object and then get rid of it. As Gramps passes, Jesse embraces him.
The film ends with the revelation that Jesse used the skull to travel back into the Old West, where he, Charlie and the rest of their friends drive off in a wagon on a new adventure, leaving the crystal skull behind, marking Gramps' new grave.
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