Yumi Ikoma and Ryou Masaoka are children who have been selected to take part in a top secret mission, to be the pilots of the first Fafner combat units; the last chance of survival for the human race. The enemy is ruthless, remorseless and is able to read the minds of humans. Therefore, the details of this mission are kept a secret even from the personnel involved. The young pilots must use all their courage and faith in order to survive and complete their mission or the fate of mankind would be compromised.

Miura Kyoji, a dedicated kendo student, discovers that his shisho (master) Tate Masanari is a reincarnated Incan warrior named Yawaru who wishes to destroy the world to purify it. Kyoji himself is the warrior Bilka, who foiled Yawaru's plans in their previous lives. Yawaru gathers other awakened spirits to release the powers of nature. Now Kyoji must wrestle with his own fate and decide if he is merely a vessel for the reincarnated soul or if he is truly Miura Kyoji and which will be better able to save the world and the future as he knows it.

In the year 2003, Professor Tenma is distraught when his son Tobio is killed in a car accident. He loses himself in his latest project, creating Atom, a robot boy programmed to be forever good. Upset that his Tobio-substitute can never grow up, Tenma sells Atom to Ham Egg, the cruel ringmaster of a robot circus. Atom meets the kindly Professor Ochanomizu, who adopts him, inspires him to become a crusader against evil, and eventually builds him a robot "sister," Uran.

A tranquil forest and all of its residents must face the destruction of man. A squirrel, born and raised in the forrest, fights to defend his home and faces trials and adversities along the way.