Following the events of Senki Zesshou Symphogear G, Hibiki Tachibana, Tsubasa Kazanari, and Chris Yukine continue to operate under the command of Genjuurou Kazanari. Meanwhile, Maria Cadenzavna Eve, Kirika Akatsuki, and Shirabe Tsukuyomi are taken into protective custody. With peace restored, everyone returns to their daily lives; however, the appearance of the alchemist Carol Malus Dienheim and her subordinates—the Autoscorers—threatens to draw everyone back into a conflict. Armed with a strange and magical power, Carol wishes to initiate the apocalypse and bring destruction to the world... and she is willing to sacrifice everything to do so. Against this mysterious new foe, the six Symphogear wielders must rise to the challenge in order to protect what they hold dear. However, will Carol and her Autoscorers prove to be too much to handle in this fight to protect the fate of the world?

Saddled with amnesia, Yuuri awakens on an interstellar cruiser drifting through space. Unfortunately, a lack of memories is the least of Yuuri's problems. Among the four other crew members is a Gnosia: a Gnos infectee whose goal is the eradication of humanity. The Gnosia appears human in all other respects, so the uninfected have little choice but to vote on whom they suspect to be the enemy, hoping to neutralize the Gnosia by putting them into cold sleep. If the Gnosia survives the vote, they will eliminate one crew member during the cruiser's following warp, when only the Gnosia remains conscious. Voting quickly proves to be an unreliable strategy, and Yuuri is left one-on-one with the Gnosia. Just when all hope seems lost, time seemingly loops back to when Yuuri first awakened. With each time loop, however, conditions aboard the ship change—neither the size of the crew nor the members' identities remain constant. Trapped in both time and space, Yuuri must figure out how to escape the loops and save humanity from the Gnosia.

Zashono Academy is a massive educational institution with over thirty-five thousand students enrolled across all grades. It is here that the plain and unpopular Densuke Mifune enrolls in high school. While he looks forward to blending into the crowd, circumstances change when he runs into Chiharu Shinonome, an incredibly attractive and intelligent girl who has captured the attention of all the students at the school. Witnessing the encounter between the two, Kirika Misono pressures them into joining her mysterious Eiken Club to compete in the school's annual club tournament. The tournament causes Densuke to become more intimate with his fellow club members, but will he be able to maintain his composure or will he give in to their bold advances?

In the near future, 10 percent of the population will consist of Humanoids—machines with advanced functions and artificial intelligence resembling human personalities, easily recognized by their sideways pupils. These specialized patients likewise require a special doctor. By day, Dr. Hikaru Sudou runs a medical clinic for Humanoids; by night, under the moniker of Moggadeet, he performs illegal procedures and gathers information about his lost mother. Hikaru encounters patients with varying problems unique to this society: a Humanoid struggling with the question of whether she and the source of her backup data are the same person, a teenage Humanoid who cannot improve athletically, and even a robot teddy bear with memories of multiple owners. As the world's technology constantly evolves, newer and more complex questions surrounding humanity arise. With each new advance, it becomes more difficult to define what truly makes one human or Humanoid.