The series takes place in the (then) futuristic year 1999. Professor Amamori discovers a 10th planet in the Earth's solar system, which he names La-Metal, while at his observatory in Tokyo. Its diameter is 9 times that of Earth. Amamori notes the planet has a highly eccentric orbit and, as it emerges behind the distant Pluto, Amamori realizes that La-Metal is on a collision course with Earth. He calculates that the planet will impact Earth on 9 September 1999, at 9 o'clock, 9 minutes and 9 seconds.

It turns out that La-Metal orbits the Solar System every 1,000 years, but only this time it is fated to come dangerously close to Earth. While damage to the giant ice-covered La-Metal would be minimal, Earth would be destroyed by the planet's massive gravitational pull. La-Metal is inhabited by a subterranean humanoid species ruled by a mysterious Holy Queen, Larela. She plans to abduct a large number of humans before the destruction of Earth, and enslave them with the help of her operatives already on Earth. These operatives are led by Promethium II, a woman known as a Millennial Queen who goes by the Earth name, Yukino Yayoi. She has been living on Earth for almost 1,000 years, like many such Millennial Queens before her, with the intention of establishing a colony for her home planet.

Promethium, who comes to care for her Earthling foster parents and friends, begins to question the La-Metalians' plans. As Yayoi, she begins working for Professor Amamori and decides to offer her help when Amamori discovers that La-Metal heading for Earth. The professor's young nephew Hajime, whose parents are killed while designing a spaceship to help a small group of humans escape from Earth, also joins their fight to save the planet.

They are soon confronted by a sabotage campaign initiated by a group of La-Metal generals against Earth. As the two planets come closer to colliding, Yukino finds out that a black hole is to blame for La-Metal's orbital deviation. A desperate plan is undertaken to destroy the black hole and save both their worlds.