During a concert by idol group Zwei Wing, an alien force known as the Noise attack the stage. Group members Tsubasa Kazanari and Kanade Amou suppress the attack using their Symphogear armor, but despite their best efforts, innocent bystander Hibiki Tachibana is fatally injured. Distraught and much to Tsubasa's dismay, Kanade sacrifices herself in the process to save Hibiki. Two years later, Hibiki lives on. Tsubasa now fights alone. With the threat of the Noise increasing, Hibiki finds herself encountering the Noise once again but this time she is granted a chance to become attuned with the same Symphogear that Kanade wielded.

After the Luna incident, Tsubasa Kazanari and foreign idol Maria Cadenzavna Eve perform a joint duet together. Much to everyone's surprise however, Maria makes a declaration of war against the world with her own dark Symphogear. Hibiki, Tsubasa and Chris are tasked with stopping Maria, Kirika and Shirabe.

After the Frontier incident, everyone who knew the circumstances believed the Noise were gone and the pain they caused was at an end. But a new conflict approached unseen. In the Yokohama Harbor Oosan-bashi Pier, a new pattern is detected that is similar to the Noise. A combat group wielding mysterious technology stands in the way of Hibiki and the others. When she hears of this enemy of unprecedented strength, Tsubasa hurries back home from England. But the Symphogear wielders see no opening to counterattack and are forced into a difficult fight. In this situation of extreme disparity, the battle for the song that will end the world begins.

The Magical Girl Incident may be over, but the people of S.O.N.G. know that mysteries still remain. Who aided Carol in building the Château de Tiffauges, and where did its world analysis data go? When Maria and Tsubasa turn up new leads about the Bavarian Illuminati along with photos of a South American military using Alca-Noise like weapons, the girls leap into action. Once there, not only do they face a human military backed by Alca-Noise, they encounter three alchemists of the Illuminati: Saint-Germain, Cagliostro, and Prelati. Proudly declaring that they have manifested a new kind of power through the sacrifice of lives, they likewise state their reasons: nothing less than world revolution!

A sarcophagus rises from the depths of a lake during a snowy midsummer. A relic of the precursor civilization, and one containing the most revered of the dead: the remains of an Anunnaki. While S.O.N.G. may have hoped for answers, the recovery of the body only signals the start of a new battle. Monsters, gods, and curses surround Hibiki and her friends, and some of those new threats look far too familiar for comfort. While struggling with doubt, pain, and loss, can the girls let courage bloom, even so? Or will the loneliness that comes from humanity’s discord overwhelm them?