Tatsumiyajima is the central island in the middle of a small cluster of islands, in a sleepy backwater of the Japanese isles. Not much happens there, and the island's young people go to school knowing that their lives are likely to remain peaceful and undisturbed. Or so they have been taught... but the truth is different. The fate of mankind is on the line, and Tatsumiyajima is the last line of defense against a hostile and incomprehensible enemy. At the center of it all, fighting for Humanity's continued existence, is the giant robot Fafner, the dragon that guards this final treasure of mankind.

Kannazuki no Miko begins in the village of Mahoroba, where time passes slowly for both man and nature. Two students from the village's prestigious Ototachibana Academy might as well be night and day. Himeko is shy and unassertive, while Chikane is bold and elegant. Despite this, they love each other, and nothing can come between them, no matter how hard they try. On the two girls' shared birthday, a sinister voice corrupts one of their friends into attacking them, and just when it seemed grimmest, the lunar and solar priestess powers that lay dormant in the two girls awaken, dispelling the evil. That was only the first hurdle, however. The two must now fend off the countless others who would threaten their well-being—even the people closest to them!

Yuna Kagurazaka, a clumsy and sweet sixteen year old girl, had her life drastically changed when she won an intergalactic contest for the person with the purest heart. Now, she is an intergalactic superhero and magical girl known as the Savior of Light. She pilots the mecha El Line to maintain the peace of the universe. But Yuna’s entire world is shaken when she is wrongfully accused of destroying a city with El Line. She is captured and taken prisoner by Misaki Ichijouin, a special agent from the Galaxy Alliance. However, Misaki soon realizes that she has been deceived, and teams up with the rest of Yuna’s friends to free the Savior and save the galaxy before an evil force is restored to power.

Just when everything seems peaceful again for Yuna and her friends, a new enemy appears in the form of three robotic sisters. Yuna must once again become the Savior of Light to fight this strong, new evil.