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 time Kida loses her doll, the Queen stops and tells her to leave it behind as there is no time. Soon she was caught in the light and bonded with the crystal, and she was carried toward the Heart of Atlantis as her daughter look on, crying. While she was carried toward the crystal, she unknowingly takes her daughter's bracelet with her, and the city soon vanishes beneath the sea.
Many thousands of 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 to 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 Atlanteans' 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 consciousness 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 -- which is what happened 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 holding the bracelet that her mother took years ago when the city sank.
The Queen of Atlantis was voiced by uncredited Cree Summer, who also voiced Kida.
It's possible that ihe Queen became a part of the crystal or its power, since Kida was holding her bracelet her mother took with her when she is carried towards the crystal.