Asaba Naoyuki is an ordinary high school student. As a member of his school's press club, he's just spent the summer camping outside the local military base, in hopes of seeing the UFOs that are secretly kept there, according to local legend. Returning to school, he meets a strange girl, Iriya Kana, and gradually comes to realize that she is more than merely strange - and that a dark secret lies beneath the world that he knows.

Because of non-stop environmental destruction, the United Nations commission a private company, "Eternal Earth", to create an artificial jungle to be a nature preserve and to protect animals. Leo, son of Panja, is born in this artificial world. The story starts when Leo and Kenichi, the son of the Eternal Earth company's CEO, meet. Kenichi has the ability to understand and talk to the animals.