Years after taking up normal lives incognito, the cyborgs are forced to fight again when the superhumans known as the Blessed appear with a plan for humanity.
The year is 2242. Kanata wants to be a Drifter and meets Noir, who is a dud Magus with no memories. However, because Noir excels in battle against the Enders, Kanata partners with her and discovers exactly what it takes to be a Drifter.
In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations.
Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Can Phos's seemingly mundane assignment lead both Phos and Cinnabar to the fulfillment they desire?
Schoolgirls discover that they have been given the ability to materialize weapons and control robotic beasts called "Children" to stop an evil organization from their plans of domination.