Queen Millennia

Every 1,000 years, Lar Metal, a huge planet that is home to an advanced civilization, passes close to Earth, bringing chaos and disaster to the smaller planet. The Millennial Queen, a native of Lar Metal, went to earth to observe the passing. The time for Lar Metal's next passing draws near, and the signs are not good. Lar Metal is to pass closest to Earth on September 9, 1999, at 9:09:09 (a reference to GE999) and bring about near-apocalyptic destruction. Time is running out as Professor Amamori struggles to see what can be done to save humanity. Meanwhile, his assistant, Yukino Yayoi, begins a course of her own, one which only she knows. Together with Professor Aramori's nephew, Hajime, she also hopes to save Earth...for though she is the Millennial Queen, she is no longer able to stand idly by and watch her homeworld bring unnecessary destruction.

Synopsis from Anime News Network