Queen Millennia (1982) on Netflix

In the year 1999, astronomer Professor Amamori has discovered a tenth planet within the solar system. Unfortunately, he also discovers that it is set to collide with the Earth on 9 September 1999, at 9:09:09 AM. Professor Amamori makes preparations to save the planet, aided in his campaign by his nephew Hajime and his secretary Yukino Yayoi. Unknown to anyone, Yayoi harbours deep secrets: LaMetal crosses paths with Earth (and wreaks chaos) every millennium, it is home to an advanced civilization who enslave any human survivors of the cataclysm, and she herself is the Millennial Queen, a special citizen of La Metal who comes to Earth every 1000 years to prepare for the this passing. However, she also hopes to save Earth, for though she is from LaMetal, she cannot stand aside and let her home world destroy the planet and its natives that she has come to love. And so she begins a desperate struggle of her own.