Galaxy Express 999: The Starlit Sky is a Time Machine(2007)

Ginga Tetsudou 999: Hoshizora wa Time Machine

Sometime in the 21st century on the earth Galaxy Express 999 destined for Great Andromeda is about to depart. A mysterious girl, Jula, suddenly appears in front of Maetel and Tetsuro who are visiting a museum. After predicting the fall of the human race, Jula has disappeared into outer space. Matel and Tetsuro follow her riding in the 999. Tetsuro finds Jula on asteroid Itokawa, which was once explored by the Hayabusa probe. Jula disappears into space again but her spacecraft crashes into an asteroid, falling down to Jupiter. Will Tetsuro be able to rescue Jula? What does Jula mean by the "fall of the human race"? Transcending space and time, this is the saga of the 999 traveling among the stars in our solar system.

(Source: corp.toei-anim.co.jp)