On the outskirts of a small town there is a rock formation called Witch Mountain rumored to possess mysterious powers. A young waitress, Zoe Moon, finds and notices infant twin children Anna and Danny, who create a wave of purple energy when their hands touch. Before she can do anything, the children are separated when a hermit, Bruno, places Anna on a truck but flees when he is spotted by Sheriff Bronson. Danny spends the next nine years of his life between foster families and frequently runs away. After his latest attempt is thwarted, his frustrated social worker decides to leave him at an orphanage run by Lindsay Brown. He is reunited with Anna when she saves him from Xander, an older boy at the orphanage who has a soft spot for Anna. Neither Danny or Anna are initially aware of their relationship, despite performing identical odd mannerisms. However, their newly found proximity to one another reawakens their supernatural powers and they realize that they are siblings. When Edward Bolt, a local magnate seeking to develop the nearby Witch Mountain, notices their powers, he decides to care for both of them as their foster father. Though Danny is happy with the development because he has his sister and a nice home, Anna is apprehensive about being adopted by Bolt and befriends Bolt's chauffeur, Luthor, who feels he has a connection to the twins. During one of their outings to a purple general store, Anna uses her telekinetic abilities and catches the attention of the store's owner, Waldo Fudd. Waldo reveals he has the same abilities they do and that they are extraterrestrials from another world where everyone has a twin. When they came to Earth to explore, everyone separated due to the quarrels they experienced on Earth. Waldo has been working to reunite them all and take them home. Meanwhile, Zoe sees the purple light from the front of the shop and recognizes it and confronts Waldo to discover the fate of the twins she saw years earlier. Though he dismisses her claims, Waldo leaves her clues regarding Anna and Danny's fates if she wishes to help them. Bolt reveals his true intention to exploit the twins' power to blast open Witch Mountain without explosives in order to obtain its valuable rock material, despite Waldo's protest that the mountain must not be tampered with. Anna discovers the truth and telepathically warns Danny, only to be held hostage by Bolt so that Danny will do as he asks. The twins are rescued by Xander and escape to Waldo's shop on a horse that Danny communicates with to help them. Lindsay becomes suspicious of Bolt when he sends the police to retrieve the children from the shop. Zoe and Bruno help Danny and Anna escape to Witch Mountain after the twins levitate Bruno's truck, while Bolt is arrested by Bronson after Luthor exposes Bolt's plot. At Witch Mountain, Waldo and the other reunited twins await Anna and Danny so they can all return home. The last set of twins arrive soon after - Bruno and Luthor. Using Waldo and his twin's power on their home world, all of the twins return home in pairs, with Anna and Danny going last to close the gate between their home world and Earth. Waldo casually comments that he will be waiting for the next group of tourists, while Anna and Danny float up into the purple smoke to Witch Mountain. Zoe narrates that Witch Mountain is not haunted but has light in it.
