When the film begins an explosion triggers a massive tidal that threatens Atlantis; all of the city is evacuated, and the royal family is being lead to a refuge. During the chaos Kida loses her doll, and the Queen tells her to leave it as there is no time. Soon a big star comes through the sky and the Queen is caught in a hypnotic blue light and is lifted towards the Heart of Atlantis while her terrified daughter and husband look on. While ascending she unknowingly takes her daughter's bracelet with her; the city soon vanishes beneath the sea.
Many thousands years later, Atlantis has fallen into ruin and the King has become more bitter and depressed since the loss of his wife. Kida says that she remembers the day she lost her mother and that she misses her very much.
When Milo Thatch and his friends arrive in Atlantis, Kida takes interest in Milo because she thinks that he can explain her some underwater murals that the natives have forgotten about. Milo explains Kida that what she saw as a girl that took her mother away was the Heart of Atlantis that gives life to the city through the Atlantean's crystals. During the film's climax Rourke mortally wounds the King to tell him of the location of the Heart of Atlantis, Milo tends to the King's wounds and he explains Milo that the Heart has developed concisouness and when it senses that Atlantis is in danger it will choose a member of the royal family to merge with and create an energy force field to protect the city, this is what happend to the Queen many years ago. Rourke and Helga find the Heart in a secret chamber underneath the throne room taking Milo and Kida hostage, the crystal senses danger and merges with Kida (just as the Queen did many years ago). It is likely that Kida could finally reunite with her mother because when she descended from the Crystal, Kida was wearing the bracelet that her mother took years ago when the city sunked.