Saiga is a normal high school student with a gift in mathematics. His daily routine is disrupted when his family gets news that his Father's remains have been discovered—a noted archeologist and researcher who had gone missing while exploring a site many years before. Among his remains were notes and artifacts that needed to be identified by the family near a notable triangular mountain in Japan known as "Japan's pyramid", a place suspected by some to be man-made. A meteor containing a strange robotic lifeform falls from the sky and begins to cause destruction, putting Saiga in danger and causing a mysterious bracelet from his father's research to activate and merge him with an ancient robot burried within the pyramid—a robot the runes describe as Reideen. It is now up to Saiga and guardian Reideen to fight against this unknown alien threat from the sky. (Source: ANN)

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. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems. [Written by MAL Rewrite]

After the battle with the Witch Cult, Subaru travels back to Crusch's manor with Emilia, when he discovers, to his horror, that everyone has forgotten Rem. Earlier, she and Crusch were ambushed by the Sin Archbishops of Gluttony, Lye Batenkaitos, and Greed, Regulus Corneus. Although they fought fiercely, both ended up having their existences eaten by Lye. This caused Rem to fall into a coma, with noone but Subaru remembering her, and Crusch lost her memories. After learning what happened, a devastated Subaru commits suicide in hopes of going back in time to before the ambush to prevent it. However, it fails as he returns to after the ambush had already occurred. Subaru later attends a meeting with Emilia, the amnesiac Crusch, Felis and Wilhelm. After a heated discussion, they decide to continue their alliance. After the meeting, Emilia comforts Subaru as he grieves for Rem.

High school student Sakura Mamiya and impoverished death god Rinne Rokudou continue to confront the supernatural. Pulled into the problems of their quirky acquaintances, the pair again find themselves immersed in trouble. Ageha's black cat Oboro seeks revenge for alleged mistreatment and demands Ageha to nullify their contract. When she refuses to do so, a bitter quarrel breaks out between them. Meanwhile, the scheming Damashigami Company shows no sign of halting its wrongdoings, and the bat-like demon Masato continues to commit devious acts to pursue his long-awaited revenge on Rinne. For Sakura and Rinne, these paranormal complications never seem to end. As their saga continues to unfold, they must cope with these unusual circumstances as they appear, all while facing problems of their own. [Written by MAL Rewrite]