In the year 2062, Earth finds itself fiercely battling Artemis—an AI which rebelled against humankind following a grand-scale workforce automation project failure years prior. In the hope of winning the war, a group of three highly skilled human warriors is assembled, known as the guardians of humanity. Empress, the last surviving guardian, wakes up alone in an empty research facility. Unable to recall anything from the past except a place called "Lighthouse No. 8," she begins to search for answers. It is not long before she discovers an impending threat from Artemis—and she is the sole person who can save the world from destruction.

What do an alien, former ninja, weak telepath, and boy pretending to be a girl have in common? They are all classmates at Kashihara Girls' Academy, and they hide their true identities from the world. Rikka, Chiyo, Sekine, and Tsubasa seem like the best of friends, but they each harbor a monumental secret that they cannot reveal, no matter what. In order to continue masquerading as normal middle school girls, each of them must invent creative ways to conceal their true selves. But that is easier said than done, as the four students end up entangled in numerous shenanigans along the way.

High above the realm of man, the gods of the world have convened to decide on a single matter: the continued existence of mankind. Under the head of Zeus, the deities of Ancient Greece, Norse mythology, and Hinduism, among others, call assembly every one thousand years to decide the fate of humanity. Because of their unrelenting abuse toward each other and the planet, this time the gods vote unanimously in favor of ending the human race. But before the mandate passes, Brunhild, one of the 13 demigod Valkyries, puts forth an alternate proposal: rather than anticlimactically annihilating mankind, why not give them a fighting chance and enact Ragnarök, a one-on-one showdown between man and god? Spurred on by the audacity of the challenge, the divine council quickly accepts, fully confident that this contest will display the utter might of the gods. To stand a chance against the mighty heavens, Brunhild will need to assemble history's greatest individuals, otherwise the death knell will surely be sounded for mankind.

After being sent to investigate the alarming disappearance of four bloodline limit-wielding ninjas from different countries, Kakashi Hatake, Naruto Uzumaki, Sakura Haruno, and Sai successfully discover their whereabouts and inform the Hokage. Unexpectedly, Tsunade's further arrangements fall apart when Hiruko—the mastermind behind the incident and also a former Konohagakure ninja obsessed with power—appears to announce that he has absorbed the missing ninjas' unique abilities. On the verge of becoming invincible, he seeks one more bloodline limit before starting an all-out war to take over the world.

As Konohagakure's past connections with Hiruko raise suspicions among the nations about its involvement in the affair, Tsunade receives an ultimatum to solve the crisis. Left with no other choice, she decides to follow Kakashi's lead after he presents a daring yet salutary scheme—a proposal that could send him to certain death. However, Naruto opposes such a plan! Despite the Hokage's decision, he is determined to save his teacher's life, even if it means fighting friend and foe alike.

[Written by MAL Rewrite]