The year is 2062. Earth has been left in ruin after the failure of a labor automation project when the AI called Artemis waged war against humanity. A girl, Empress, awakens in a research lab. As one of the three surviving guardians, she must destroy the Orbital Elevator before Artemis can complete its construction. Failure will result in a machine army overrunning Earth.
Twenty years have passed since the failure of Project Elysion, a massive workforce automation project. Artemis, the artificial intelligence at the core of the project, had chosen to attack humanity, and Earth has been devastated ever since. A girl named Empress wakes up in the base of an underground research facility, having lost all memory of her past. She meets a young brother and sister duo named Norito and Miya, who came to the base to collect precious water. Empress aims to reach the surface together with the two of them, but she comes face-to-face with many different enemies, and Empress soon finds herself cornered...
Empress had made the decision to take Norito back to the mountain town where he and his sister live. Along the way, she was suddenly attacked by Strength, her supposed ally. Empress tries to fight back with a powerful weapon summoned from her right arm, the Coilgun, but the weapon doesn't work due to lacking the necessary energy. Placed at a disadvantage, Empress leaves to escape. She arrives at the mountain town and is then asked by Norito to help bring essential supplies from the nearby site of a former hospital. However, there lays a very dangerous beehive.
Empress and the others saw countless lights headed in the direction of the Peacebuilding Forces base. The lights were from armed vehicles belonging to the Education Institution, a cult that commits genocide while claiming to educate ignorant fools. Believing they were coming for her, Empress headed straight for their vehicles herself. However, the Education Institution were not after her, but a girl named Momiji who had escaped from them, and Empress and the others ended up rescuing her. Momiji then asks them to help her friends, who were being taken for a ritual in three days' time on one of the Education Institution's freight trains. Suddenly, Empress' right arm is shot off by an unknown sniper. The shot came from Dead Master, a girl wielding a large sniper rifle from about a kilometer away, and one of Empress' former allies.
Empress and the others find out from Major Volt that they've only got one month until the Orbital Elevator is complete. The Dead Master engages negotiations and an ambush occurs. Charlotte, an enhanced human, is released by the Educational Institution. Empress attempts a counter-attack, but the colonel stops her.
A chance meeting leads Norito to seek Strength`s help. He wants her to call Empress because Miya has been taken by the Educational Institution and is being used as a prize in a game. They are suddenly pursued by soldiers and Strength purges a side of her arm. Strength`s personality changes.
Strength and Norito burst into the enemy's aircraft carrier to save Miya. Empress and the others engages in battle with a squadron of armed guard vehicles. In the laboratory on the carrier, the bodies of dead girls are piled up like trash after having failed adaptability experiments. They find Miya tied up, but they also find Lunatic, Artemis' avatar.