Ghost hunter Cyrus Kriticos (F. Murray Abraham) and his psychic assistant Dennis Rafkin (Matthew Lillard) lead a team on a mission to capture a spirit called the Juggernaut (John DeSantis). Several men are killed, apparently including Cyrus. However, the team is able to catch the ghost. Cyrus's nephew Arthur (Tony Shalhoub), a widower, is informed by Cyrus's estate lawyer, Ben Moss (J. R. Bourne), that he has inherited Cyrus' mansion. Financially insecure, Arthur decides to move there with his two children, Kathy (Shannon Elizabeth) and Bobby (Alec Roberts) and their nanny Maggie (Rah Digga).
Posing as a power company inspector, Dennis meets the family and Moss as they tour the mansion. The residence is made entirely of glass sheets inscribed with Latin phrases, which Dennis recognizes as barrier spells. While searching the basement, Dennis is hit by psychic flashes and discovers the twelve angry ghosts he and Cyrus captured are imprisoned in the house, held captive by the spells. As Dennis warns Arthur, Moss slips downstairs and picks up a valise of cash, unwittingly triggering a mechanism that seals the house and releases the ghosts one by one. He dies when a set of sliding doors snaps shut, cutting him in half. Bobby slips away from Kathy and Maggie and enters the basement, where he sees several of the ghosts, particularly that of the Withered Lover - his mother Jean, who had died of injuries sustained in a house fire. He is knocked unconscious and dragged away.
Using a pair of spectral glasses that allow the wearer to see into the supernatural realm, Dennis convinces Maggie that the ghosts are real. Dennis discovers that the Jackal, one of the most dangerous of the twelve ghosts, has been released and that the family is now in grave danger. The Jackal attacks Kathy when she and Arthur enter the basement in search of Bobby, but they are saved by Kalina Oretzia (Embeth Davidtz), a spirit liberator who is attempting to free the ghosts. Kathy disappears soon afterward, and the four adults gather in the library, where Arthur learns that Jean's ghost is trapped in the house. Kalina explains that the house is a machine, powered by the captive ghosts, that can allow its user to see the past, present, and future. The only way to shut it down, she says, is through the creation of a thirteenth ghost from a sacrifice of pure love. Arthur realizes that he must become that ghost by dying to save his children.
Armed with a pane of the special glass, Arthur and Dennis enter the basement to find the children. Dennis barricades Arthur into a corner behind the glass, protecting Arthur but allowing two ghosts, the Hammer and the Juggernaut, to beat Dennis to death. It is then revealed that Cyrus faked his death to lure Arthur to the house; Kalina is his secret partner. Cyrus has orchestrated the abduction of Kathy and Bobby so that Arthur will become the thirteenth ghost, which will not stop the machine as Kalina had claimed, but trigger its activation. Cyrus kills Kalina and summons the ghosts to activate the machine.
Arthur arrives at the main hall and witnesses all twelve ghosts orbiting a clockwork device of rotating metal rings, with his children at the center. Discovering Cyrus' true fate, Arthur fights Cyrus while Maggie disrupts the machine's controls. The ghosts hurl Cyrus into the rings, slicing him to pieces. With the encouragement of Dennis' ghost, Arthur jumps into the machine, avoiding the rings and saving his children. The walls of the house shatter as the malfunctioning machine rips itself apart, freeing the ghosts. Dennis smiles at Arthur and departs, and Jean's ghost appears before the family and tells them that she loves them before she and all the other ghosts disappear.
As the family leaves the house, Maggie exclaims that she is quitting.
The first twelve of the thirteen ghosts that make up the fictional "Black Zodiac" each have their own unique background stories. Although these stories were not described in the film, the production and make-up teams explain their guidelines on the DVD special feature "Ghost Files". Cyrus narrates each ghost's back story. They also seem to increase in danger as their numbers increase.
1. The First Born Son – The First Born Son is the ghost of Billy Michaels, a boy who loved cowboy films. A neighbor challenged him to a duel, using a bow and a real steel-tipped arrow against Billy's toy gun. Billy died when the neighbor shot the arrow through the back of his head. Billy's ghost is dressed in his cowboy suit and holding a tomahawk, with the arrow still protruding from his head. His ghost whispers "I want to play" or "play with me".
2. The Torso – The Torso is the ghost of a bookie named Jimmy "The Gambler" Gambino. When Jimmy found himself unable to pay off a Mafia-connected client's large winning bet on a boxing match, the client cut him into pieces, wrapping them in cellophane and dumping them into the ocean. His ghost appears as his decapitated, legless torso, trying to walk around on its hands as the head lies screaming on the floor.
3. The Bound Woman – The Bound Woman is the ghost of Susan LeGrow, a girl with a wealthy background and a penchant for playing with boys' affections. On the night of her high school prom, a football player she was dating caught her with another boy; the next morning, the boy was found dead and Susan went missing. She was later found buried at the 50-yard line of the school's football field, strangled to death; the player was convicted of her murder and executed. Her ghost is wearing her prom dress and is hanging from the ceiling with her arms tied.
4. The Withered Lover – The Withered Lover is Jean Kriticos, Arthur's wife. She was burned severely while saving her family from a devastating house fire, and died of her injuries in the hospital. Her ghost initially appears in a hospital gown, hooked up to an IV pole and showing severe burns on her face. However, after the destruction of the machine, her ghost is wearing her normal clothes and her burns have vanished. Unlike the other ghosts, she is not a vengeful spirit and tries to help her family.
5.The Torn Prince – The Torn Prince is the ghost of Royce Clayton, a 1950s high school baseball star with a bad attitude and a superiority complex. During a drag race, he died when his car spun out of control. His ghost carries a baseball bat, and parts of his face and body are torn to shreds from being dragged underneath his car. He uses the bat as a melee weapon, and while inside his containment cube, he sits atop the wreckage of the car.
6. The Angry Princess – The Angry Princess is the ghost of Dana Newman, a young woman with striking physical beauty but the inability to recognize it. Driven to depression by a string of abusive boyfriends, she began to work for a plastic surgeon who paid her in cosmetic procedures. One night, she tried to perform surgery on herself, but the attempt left her blind in one eye. She committed suicide in the bathtub by cutting herself with a butcher knife until she bled to death. Her ghost is naked, still holding the knife and showing all the self-inflicted wounds, and her cube is drenched in blood.
7. The Pilgrimess – The Pilgrimess is the ghost of Isabella Smith, a 17th-century New England colonist who was shunned by other settlers. Accused of witchcraft by the town preacher after livestock began to die from an unknown ailment, she fell under further suspicion when the preacher himself succumbed. The townspeople trapped Isabella in a barn and set it on fire, but she emerged without any injuries; they then locked her in the pillory and left her to starve to death. Her ghost still has the pillory's yoke locked around her hands and neck.
8 and 9. The Great Child and The Dire Mother – The Dire Mother is the ghost of Margaret Shelburn, a woman whose diminutive height constantly attracted stares from others. She joined a carnival freak show, but was raped by one of the other members and gave birth to a son, Harold (The Great Child). Margaret spoiled Harold throughout his life, so that he always wore diapers and had to be spoon-fed even as he grew to a vast size and weight. Carnival workers kidnapped Margaret as a prank, but she suffocated to death by the time Harold found her. He flew into a rage and killed the culprits with an axe, putting their remains on public display, and was in turn killed by an angry mob. Their ghosts are always together, with Harold wearing a food/vomit-splattered bib and carrying the axe, while Margaret sometimes feeds him.
10. The Hammer – The Hammer is the ghost of George Markley, a blacksmith who lived in a small town in the 1890s. He was wrongfully accused of stealing, and refused to leave town when threatened with exile. A gang led by his accuser hanged his wife and children; in revenge, George used his blacksmith's hammer to beat his accuser and the other culprits to death. The townsfolk executed George by chaining him to a tree, driving railroad spikes into his body, severing one hand, and attaching the hammer to it. His ghost is still pierced with the spikes and wrapped in the chains, and he wears the hammer in place of his missing left hand.
11. The Jackal – The Jackal is the ghost of a 19th-century man named Ryan Kuhn, who began attacking prostitutes as an adult. He committed himself to an asylum in search of help but eventually went insane. The doctors kept him permanently bound in a straitjacket, causing his limbs to contort horribly until he gnawed through it. Ryan was then confined to a basement, with a metal cage locked around his head, and grew to hate all human contact. When a fire broke out, everyone but Ryan escaped; he chose to remain behind and let himself be burned to death. His ghost wears the loosened straitjacket and head cage, whose front bars have been snapped apart.
12. The Juggernaut – The Juggernaut is the ghost of Horace "Breaker" Mahoney, a serial killer of enormous height, strength, and grotesque appearance. Abandoned as an infant by his mother and ostracized by everyone, he eventually got a job crushing cars in his father's junkyard. After his father died, Horace went insane and began bringing hitchhikers and stranded drivers to the junkyard, breaking all their bones and tearing them apart with his bare hands to feed to his animals. One of his potential victims was an undercover police officer, who called for backup and brought a SWAT team to surround the junkyard. Horace killed three officers before being shot to death by the team. His ghost still wears the bullet-riddled clothing from the night he was killed. Dennis Rafkin and Cyrus Kriticos note that Horace killed nine people while he was alive, then 31 more as a ghost; Horace kills several of Cyrus' assistants in the attempt to capture him, then later kills Dennis as well.
13. The Broken Heart – The thirteenth ghost would have been Arthur Kriticos himself. Cyrus planned for him to sacrifice himself out of love for his family, the final step needed to activate the house's machine.
In the US, the film opened ranking 2nd, making $15,165,355. It spent 10 weeks in the US box office, eventually making $41,867,960 domestically, and $68,467,960 worldwide.
Reviews for the film were mostly negative. Praise was directed towards the production design but the film was criticized for its lack of scares. It holds a "Rotten" rating of 14% on review aggregator Rotten Tomatoes, where the consensus was, "The production design is first rate, but 13 Ghosts is distinctly lacking in scares." Roger Ebert praised the production values saying, "The production is first-rate. The physical look of the picture is splendid." However, he criticized the story, lack of interesting characters, loud soundtrack, and poor editing. It is on his list of "Most Hated" films.