One fateful day, high school sprinter Hitomi Kanzaki experiences a disturbing vision of another world and discovers from her best friend that Amano (the track team star she has a crush on) is about to go abroad. On an impulse, she asks him the next day for her first kiss -- if she can sprint 100 meters in thirteen seconds. But then, a young warrior prince and a dragon appears before Hitomi during the run ....

In a shaft of light, Hitomi and the prince Van tranports to the world of Gaea, where Earth is known only as the "Mystic Moon" in the nightly expanse. Van returns to the capital of his country Fanelia to be coronated after obtaining the Energist crystal from the dragon. During the coronation rite, the Zaibach empire launches an invasion with Guymelef Alseides mecha, and Van must retrieve at his mentor Balgus's bidding Escaflowne, the legendary god of protection of Fanelia.

At long last, Dornkirk's vision of reviving the power of Atlantis seems realized as the Sphere of Absolute Fortune's effects spread across the battlefield and the world of Gaea. However, the war does not end as the Destiny-Altering Device only turns the combatants' bellicose thoughts into reality. Gaea's fate in the end lies in a girl from the Mystic Moon and a white-winged dragon.