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?

On the run from the Erste Empire, Gran and the crew of the Grandcypher receive an offer to negotiate a ceasefire. Meeting at the neutral territory of Albion Citadel, they are welcomed and hosted by Vira Lillie: current Lord Commander of Albion and a friend of Katalina Alize from her officer training at Albion. Imperial General Furias grants the Skyfarers an official pardon, but fails to defuse the tense situation. Given time to unwind, the Skyfarers attend a gala hosted by Vira to celebrate the arrival of the crew. However, tensions run high, as Furias and the Erste delegation remain at Albion even after the negotiations conclude. Learning about the existence of a Primal Beast on the island, the crew is shocked to discover a letter from Katalina announcing her resignation. While Gran heads off to find their former comrade, Eugen and Rackam decide to investigate the Imperial presence on the island, suspecting a more sinister scheme lying up the Empire's sleeve.

In 2008, the Japanese government began hunting people who identify as otaku in an effort to protect the country's culture. In just one week, the enforcement agency known as the SSC captured almost every otaku by force and confiscated their memorabilia. One passionate man calling himself Otaku Hero refuses to allow this agency to do as they please: he raises a resistance army made up of other displaced geeks who band together to help defend their culture. Three years later, the fires of rebellion wane as all hope seems lost for otakus. Spurred on by his ally—the magical girl Anarchy—Otaku Hero commands the resistance in an effort to reunite Anarchy with the other two other magical girls: Blue and Pink. By combining the power of this trio, the resistance may be able to defeat the SSC and save otaku culture for everyone.

Segua Kingdom has been losing the war against Ninterdo Empire but the tables are turned by the appearance of a boy called Gear. All the characters are parodies of Nintendo or Sega games such as Sonic the Hedgehog, Super Mario Bros., The Legend of Zelda etc.