Those who have both seen the movie and read the book say that the book is radically different in tone from the light-heartedness of the movie, although the premise is the same...two children from another planet crashland on earth, their special powers making them a target for a greedy man who wants to control them. One major difference is that the kids are befriended by Father O'Day, a priest who has lost much of his faith in mankind, rather than Jason O'Day, a retired man who has lost much of his faith in mankind. Because of this, the book has religious undertones that are not part of the movie. There are also anti-Communist undertones in Key's story, as the children's spaceship is shot down over Hungary by Communists, who subsequently imprison them. Tia and Tony escape the Communists and make it to a Spanish boat that is supposed to take them to America. When they arrive in America, however, Mr Deranian takes possession of them and gives them to an elderly lady they called Granny Malone to raise.
Also in the book, Tia and Tony are older, and they are not blond and blue-eyed; rather they have pale hair, olive skin, and eyes that are almost black. Because of their unusual looks and their psychic powers (telekinesis, clairvoyance, super-hearing, etc.), they are often the target of suspicion and ridicule. Although both children can communicate with each other silently, Tia is mute. (That's why she carries the star case; she keeps pencil and paper in it so she can write notes to people.) Tony later remembers that most of their people couldn't talk...he was one of the few who could. When Granny Malone died (hit by a taxi), they were sent to Hacket House, a grim orphanage/detention center run by the equally grim Mrs Grindley. The big baddie in the book is Deranian, not Bolt. He wants to take the children to France so that he can extract from them the secrets to their powers, so they run away, hoping to make it to the house of a friend of Fr O'Day in Stony Creek, somewhere in the Blue Ridge Mountains. Their flight leads them to Witch Mountain where, like in the movie, they are reunited with their people.