As the film opens, two young children are being brought to a beautiful orphanage in the countryside of California. The kids, named Tony Malone and his younger sister Tia, are warmly welcomed by the home's proprietor Mrs. Grindley, but make fast enemies with local bully, Truck. The children explain to Mrs. Grindley their background; when they were very small, they were adopted by an older couple named Mr. and Mrs. Malone. They have no memory of their parents, or really anything before being taken in by the Malones, though Tia has carried around a small box with two stars emblazoned on it for years, her "star case", and occasionally has obscure memory flashes to some kind of accident. Now that both of their adoptive parents have died, the pair have been sent to live in the orphanage. Tony makes friends playing softball, while Tia befriends a black cat, which they name Winkie. While playing baseball, Tony makes an incredible leap to catch the ball and strike Truck out. Truck accuses Tony of cheating, and attempts to beat him up, but Tony stops him by making a baseball glove punch Truck, and levitating a bat so Truck strikes it and hurts his hand, while Tia looks at Tony with disapproval. The other kids stare at the pair, and Tia telepathically chastises Tony for showing off. That night in bed, Tia reminds Tony how they were looked upon as freaks by the other kids back in their old home, and even feared by the community until they stopped doing the "spooky stuff". The kids also realize that they can hear "the dogs" barking again, from miles away. They take this as an ill omen for times to come. Some time later, all the children are awaiting a bus to go see a movie in town. Truck steals Tia's star case and threatens to destroy it unless Tony fights him for it, though Winkie knocks it out of Truck's hands and defuses the situation as the bus arrives. After the movie, Tia has a premonition of danger involving a man about to get into his car across the street. They separate from the group to warn him, and are collected by Mrs. Grindley. The man, named Mr. Deranian, decides to go for a walk instead, and moments later his car is plowed into by a runaway truck, exactly where Deranian would have been sitting. He stares in awe as the children leave. Deranian returns to his employer, Aristotle Bolt, a millionaire who is obsessed with finding supernatural means of expanding his wealth. Deranian tells him of his encounter, and Bolt tells him to bring the children to him. Tony is playing his harmonica to draw a picture of a place he's been having visions about. Tia walks in to show him her damaged star case, but while inspecting it, they find the front panel slides away to reveal a map to a unknown location, and landmarks "Stony Creek", and "Misty Valley". They determine to find their way there someday, as it may hold a clue to their past. Tia then notices the picture Tony is drawing, and they say that since they've never seen the mansion in the picture before, they must be going to it soon. Deranian researches the two after finding out their names from the orphanage, and forges many documents, which he uses to prove to Mrs. Grindley that he is, in fact, Tony and Tia's uncle Lucas, claiming that he recognized Tia as looking like his sister. Tony and Tia are skeptical, but have no choice but to go with Deranian. Dernanian takes the two far into the country, to Mr. Bolt's vast and gorgeous estate on the coast. As they drive in, they pass the gate guard, Loco, who has a severe allergic reaction on proximity to Winkie, and large kennels filled with guard dogs, that both Tia and Tony recognize as the source of the barking they heard before. Mr. Bolt plays the part of the gracious host, giving the children lavish living quarters as well as keeping them busy with a number of activities. During a riding lesson, Tia speaks to and rides a wild horse named Thunderhead, as the instructor looks on dumbfounded. Later, Tony uses his harmonica to make the marionettes in their room dance on their own. Little do they know that Mr. Bolt has been recording them on the CCTV cameras installed all over the property, intending to blackmail the children using the tapes. One night, Tony notices Tia seems upset. Although she is unable to pinpoint why, as they seem to have gotten everything they've ever wanted. Tony admits to also feeling as if something is wrong. Tia tells Tony that she has had visions of Bolt turning on them and never letting them leave, and tells him they should consider running away. Tony reluctantly agrees. While having dinner with Mr. Bolt and Deranian, Bolt runs out of patience and reveals to the children that he knows about their powers, against Deranian's advice. Tony and Tia feign ignorance, but can tell he isn't lying. Bolt tells them he wants to understand their powers, and use them to help his business efforts. The two tell him that he is not thinking clearly and needs some rest, and he leaves with Deranian. Tony and Tia are shaken at the revelation, and discuss what to do. Telepathically, they hear Bolt talking to Deranian, saying that if the children don't cooperate, he will have them sent to a secluded island in the middle of a freezing ocean to prevent them from escaping. Tia and Tony decide to run away that night, and try to find their way to the place on the star case map. After they are 'asleep', and Deranian locks their bedroom door for the night, they put their plan into action. Fully dressed and ready to go, they take Winkie, and Tia unlocks the door with ease. They take a back door out of the mansion and make it outside before alarms begin to blare throughout the compound and the dogs are set loose. They run and make it as far as the gate before the dogs catch up, but Tia empathically tells them to chase their handlers instead, then calls Thunderhead to their aid. Tony tries to use his harmonica to open the gate, but Loco is holding it closed. Winkie jumps into the guard booth, causing Loco to sneeze uncontrollably and release the gate lever. Tony opens the gate, and they all get away on Thunderhead. Bolt is furious, and asserts all of his power in the area to find the children, including state police. The kids make it to town, and see a Winnebago Motor Home parked outside a store. They hide inside the RV as the crotchety driver, Jason O'Day, loads up to leave for a road trip. Deranian drives by and asks Jason if he has seen the runaways, but Jason tells him to shove off, and drives the RV away. The next morning, Jason pulls into a beach and gets out to stretch his legs. Winkie finds her way out, knocking a bag of flour onto the children as she does. Jason finds Winkie and takes a liking to her, but when he goes inside the RV to get tuna, he finds Tony and Tia hiding inside. He evicts them from his RV, but takes pity on them and tells them to clean up while he makes them some food. Tia tells Tony that despite his grouchy attitude and professed dislike of kids, she can tell he is a good person. State Police all over are searching for the children, and Deranian suspects that they might be hiding in the Winnebago he saw the previous night. They begin to search for the RV specifically. The kids explain their situation to Jason, who is skeptical. When Jason realizes he's lost his keys, they prove their powers to him by starting his engine without them, and having Winkie find his keys on the beach. In exchange, they convince him to take them to Stony Creek. Jason takes the RV to a gas station for supplies, but the pump attendant is acting suspicious. They leave, and when the children take note of how many provisions Jason got, he tells them the trip might not be as straight forward as they hope, as Bolt is an extremely powerful man in these parts. Just then a State Trooper on motorcycle shows up on their tail, tipped off by the gas station attendant. He pulls them over and gets off his bike, but before he can approach the Winnebago, Tony telekenetically sends his cycle over the cliff, and they drive away. Tia's memory flashes of the accident they were in when the Malones took them in have been becoming more frequent. They become clear enough for he to tell that it had something to do with the ocean, and a trawler like Mr. Malone had. Mr. Bolt calls the Sheriff of a town called Longview, and tells him a reward has been offered for the children's capture, and to be on the lookout as the RV has been seen heading that direction. The group stops for the night in a secluded campground. Jason is becoming fond of the children, and helps them decipher the landmarks on their map. The kids suspect that the place in the mountains might be where they came from, though Tia has a feeling that it was further away then that. Jason and the kids wonder why whoever gave them the star case would hide the map so well. Jason mentions in passing that he never married, but Tia reveals that to be false, stunning Jason. Both children explain that they can see from his mind his life before, how when he was a young man, he married a beautiful woman who died just a few months after they were wed, leaving Jason in despair. He swore an oath never to love anyone ever again, hence his outwardly gruff demeanor. Jason is momentarily upset at these old memories, and the children apologize for prying. In the middle of the night, Deranian and his driver Ubermann are coming the area and spot the RV in the woods. they attempt to sneak up on them, gun drawn, but Winkie hears them coming and knocks the gun from Ubermann's hand, waking the group. Tia telekenetically holds the gun on Deranian and Ubermann, while Jason starts the RV and drives away. Deranian gives chase, and Jason tells Tony and Tia to jump out at the next town, Longview, to split up and lose their pursuers. He tells them to meet him at his brother's house outside of town. They turn a corner and Tony and Tia jump out of the RV and run another direction, while Deranian's car follows Jason. Tia and Tony make their way through the town in the dark, but are ambushed by the Sheriff, who witnessed the ruse. He takes them to the station and confiscates their items, but when he takes down their names, Tony instinctively answers with the last name "Castaway", confusing himself and Tia. The Sheriff locks them up as runaways, and Tia says she thinks Tony said Castaway as a translation from another language, perhaps their original last name. Tia remembers a man named Uncle Bene was with them when they wrecked. He gave Tia the star case, but drowned while keeping them afloat. They hear the Sheriff tell his deputy that Deranian is on his way to collect to children, and Tony asks Tia to levitate his harmonica to him. They easily unlock the cell door, and Tony telekenetically makes a figure out of a broom handle, trench coat, and hat to attack the Sheriff as a distraction. They grab to star case and escape to the woods, but not before Tia frees a caged circus bear that she says needed her help. The terrified Sheriff rallies the townsmen to hunt down the pair, claiming that they are witches. Deranian arrives in the middle of the chaos and is worried the bloodthirsty townsfolk will kill the children. Tia and Tony meanwhile, have made it to the forest. They tell the bear to hide in a cave while they make their way to Jason's brother's house. The townsmen search the cave looking for the kids, but the bear scares them away. The kids finally make it to the house and meet up with Jason and Winkie, but Deranian and Ubermann are on their trail and radio Bolt. Tia and Tony fill Jason in on what they've remembered so far. They both remember that they are supposed to find someone named Castaway in Stony Creek. They realize the accident must have been on a ship from another country, since they didn't understand English when the Malones adopted them. But they can't remember where the ship could have come from. Jason his brother wrote to him in his letters about a group of people who had settled into a secluded place called Witch Mountain, above Stony Creek. The people there keep to themselves, and no one knows where they came from. Tony and Tia figure that they must be their people. Bolt leaves via helicopter to join the Deranian at the house. The group sees Deranian and Ubermann approaching, and leave via the back door while Tia telepathically asks the bear for help. They drive off and Deranian attempts to follow, but finds the bear sitting in his car. While driving, Tia and Tony remember more details about their past. The night their ship sank, many other people died as well as their uncle Bene. There were multiple ships however, and the survivors made it to their destination on Witch Mountain. They all fled there from a place that doesn't exist anymore, hence why they call themselves 'Castaways'. The two stars on the star case was the emblem of their old home, a place with two suns in the sky. Not another country, but in fact an entirely different planet, in another solar system. All the pieces of memory finally fit together. Their world was dying, and the remaining population boarded spaceships to escape and find a new home. Tony and Tia's ship got caught in a storm and was destroyed, and Uncle Bene helped the children survive long enough to be rescued by the Malones, who took them in. They suspect that they are the only ones on their spaceship who made it. Bolt arrives in his helicopter to the house, which scare the bear away. Deranian explains the situation to Bolt, and goes to follow the RV. Jason and the kids arrive in Stony Creek, but the town seems deserted. They go to a building marked Misty Valley Cooprative, and decide to wait for someone to come back. Deranian finds the search party from Longview, and tells them the reward for the children as gone up, but they must be caught alive. One of the searchers suggests they look in the next town up the line; Stony Creek. Jason and the kids are getting restless waiting, and Tony suddenly has a feeling to check the phone book. He looks up the name Castaway and dials the number. The man on the other end of the phone rejoices when he hears Tony and Tia's names, but just then Deranian arrives with the townsmen. The voice on the phone tells Tony to take the back door, which they do. Once outside, the children hear the voice again, this time telepathically, telling them to make sure Deranian doesn't lose them, as he has a surprise waiting for him that will discourage him and Bolt from ever looking for them again. A chase ensues up the mountain, and the kids manage to hold of some of their pursuers. Deranian takes a shortcut and attempts to head them off, but somehow the RV flies into the air right over him. The force making this happen also makes Bolt's helicopter fly upside down next to them, which flabbergasts Bolt. The RV comes to a landing on Witch Mountain, and the voice tells the group to get out and wait. The kids thank Jason for all he's done, and say goodbye. Jason has become very fond of them, and asks if he could think of them as the kids he never had. Tia also asks him to take Winkie, since Jason needs a companion. The source of the voice emerges from the treeline, and the children recognize the man as their uncle Bene; he'd apparently not drowned in the storm, but survived after empathically asking a passing shark for help. Bene praises Jason as a credit to his species, and explains that there were other young survivors that are still missing, all with star cases and maps. So far, only Tony and Tia have made it. Jason vows to try and find the other surviving children and bring them home. Deranian arrives in his car, and Bolt's helicopter comes to a landing, still upside down. Bene tells them it's time to go. They children bid farewell to Jason and go with Bene. They board a flying saucer, which takes off in front of Bolt, out of his reach forever. He and Deranian leave defeated. After Bolt leaves, the spaceship comes back and flies over Jason and Winkie into the Misty Valley of Witch Mountain to join the colony.