Now Utau has left Easter and restarted her singing career, while Ikuto still remains at Easter. To replace Utau Easter hires a new character, Lulu. Lulu has the power to create question mark eggs, instead of x-eggs. Throughout this season we start to see all the love interests more so then in the first season. Tadase and Amu seem to be a couple now, but they have their problem, especially when Amu starts hiding Ikuto in her room. She lies to Tadase, her family and all the Guardians about it, which in the end causes more problems then she expected. Easter also has a new plan to control Ikuto. Using his violin Easter controls Ikuto so that he transforms into Death Rebel. The sound of his violin turns all the heart eggs with in distance into x-eggs. With a large amount of x-eggs gathered, the embryo will soon turn up. (Source: ANN) Episode numbers continue as 52, 53, 54, etc.

Amu Hinamori is a student at Seiyo Elementary, where she has a reputation for being "cool and spicy"; however, her real personality is that of an extremely shy and easily intimidated girl. One night Amu makes a wish that she would have the courage to be reborn as her "would-be" self. The next morning Amu finds three brightly colored eggs—red, blue, and green—in her bed. Each egg eventually hatches into a Guardian Character: Ran, Miki, and Su. Guardian Characters are angel-like beings that aid a person into becoming their "would-be" selves and fulfill the person's dreams. The Guardian Characters accomplish this by giving encouragement and advice, but they can also temporarily change a person's personality and abilities. With the Guardian Characters, Amu's life becomes much more complex as she now struggles to deal with her new personalities and the Seiyo Elementary Guardians—a student council group where each member has their own Guardian Character—who recruits Amu to search for and seal the X eggs and X Characters, corrupted forms of people's dreams.

It's been several years and Kyosuke Kasuga is now 19. A mysterious phone call warns him of oncoming cars but he doesn't listen. Ironically, he gets hit by a car and because of his telepathic abilities, gets sent three years into the future. His 22 year old future self is now a photographer who is lost in Bosnia and believed to be dead. Kyosuke must find his 22 year old future self and restore himself, the 19 year old, to his correct time. Along the way he reunites with Hikaru who is now a professional and famous dancer. Madoka is also there, distraught over both Kyosuke, the 22 year old, going missing in Bosnia and Kyosuke, the 19 year old, getting hit by a car.

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? [Written by MAL Rewrite]