A girl named Hibiki Tachibana attends a concert held by Tsubasa Kazanari and Kanade Amō, who form the pop duo, ZweiWing. In the middle of the concert, the stadium is attacked by an alien race known as Noise who begin killing the attendees. Tsubasa and Kanade summon mechanical battle armor known as Symphogear to fight off the Noise, but soon find themselves in a pinch. Kanade tries to protect Hibiki, but she is hit by a stray fragment of Kanade's armor. With her suit losing power, Kanade sings a song that destroys all the Noise, but at the cost of her own life. Back in the present, Hibiki, who was able to survive, is attending Lydian Music Academy alongside her friend, Miku Kohinata, while Tsubasa, who goes to the same school, continues to fight the Noise alone. As Hibiki goes into town to buy a new CD, she comes across a Noise attack and tries to help a young girl get to safety. When they become cornered, she sings a song that ends up giving her Symphogear armor.

Hibiki uses her newfound ability to protect the girl from the Noise before Tsubasa arrives on the scene to defeat them. Afterwards, Hibiki is taken to the underground headquarters for the Mobile Disaster Response Corps 2nd Division to run a medical checkup. They soon reveal Hibiki's ability to summon Symphogear comes from fragments of a relic Kanade possessed that entered Hibiki's body during the battle two years ago. As Tsubasa is shocked by the news, Hibiki agrees to fight against the Noise. A large Noise monster appears in the city which Tsubasa defeats, before telling Hibiki that she wants to fight her.

Tsubasa attempts to attack Hibiki, refusing to accept her as Kanade's replacement, but the fight is halted by 2nd Division's leader, Genjuro Kazanari. Two months later and the two have still been unable to get along with each other. As the 2nd Division discuss the recent outbreaks of Noise, they theorise the Noise are targeting a collection of relics known as Durandal hidden beneath Lydian Academy. As Hibiki makes plans to watch shooting stars with Miku, she is called away to another Noise outbreak, forcing her to cancel to both girls' ire. As Hibiki tears through the Noise, with Tsubasa arriving to finish off its leader, they are confronted by a new enemy wearing the Nehushtan armor that was stolen two years ago.

Five years ago, Kanade was brought to the 2nd Division after her family was killed by the Noise. Wanting to get revenge on the Noise, she underwent harsh medical treatment to become compatible with the Gungnir relic and gain Symphogear. As she began fighting alongside Tsubasa, she grew an appreciation for sharing her music with others and formed ZweiWing with her. Back in the present, Tsubasa faces off against the Nehushtan clad enemy, who reveals her goal is to capture Hibiki. As her opponent starts to overwhelm her, Tsubasa sings her Superb Song, which forces the opponent to retreat, whilst Tsubasa barely survives the damage done to her body. As Tsubasa recovers, Hibiki hears about how she was affected following Kanade's death two years ago and becomes depressed, feeling everything has been her fault. After some encouraging words from Miku, Hibiki resolves to be herself and become stronger to protect others and begins training with Genjuro.

As Chris is punished for the failure of her mission by a mysterious woman known as Finé, Tsubasa regains consciousness after speaking with Kanade in her dream about how she should live. Meanwhile, the Minister of Defense is assassinated by terrorists, targeting a case that Ryoko manages to recover. Ryoko explains the case contains a chip pertaining to the Durandal sword hidden beneath the base. Hibiki accompanies Ryoko on a mission to escort Durandal to a safe location, but they are soon confronted by Chris and a group of Noise which Hibiki fights off. The Durandal responds to Hibiki's voice and activates, and despite Chris's attempt to grab it, Hibiki grabs it instead, giving her a short moment of incredible power which drives off Chris.

As Chris vows to take Hibiki down with her own power, Hibiki is asked to help look after Tsubasa whilst she recovers. As Tsubasa asks to hear from Hibiki about what she fights for, Miku spots the two together and becomes determined to talk with Hibiki. When Miku ends up getting caught in the battlefield when Chris appears, Hibiki is forced to reveal her secret to save her. Luring her away, Hibiki attempts to reason with Chris, but she is unwilling to listen. Being unable to construct an Armed Gear like Tsubasa, Hibiki instead uses the required energy to power her punch and break through Chris's armor.

As Hibiki tries to reach Chris's feelings, Chris activates her own Symphogear, Ichaival, and attacks Hibiki. As Tsubasa arrives on the scene to back Hibiki up, Finé arrives and breaks up the fight, telling Chris she no longer has use for her. Later that night, Chris comes across a pair of siblings and helps reunite them with their father. Meanwhile, Miku is mad at Hibiki for lying to her, telling her they can no longer be friends. As Chris tries to confront Finé, she dons the Nehushtan and attacks her.

Whilst having a walk, Miku encounters Chris, who had become exhausted from being chased by the Noise, and decides to help nurse her back to health. As Chris explains her troubled childhood to Miku, a Noise alert appears, with Chris blaming herself for bringing them there. As Chris has trouble transforming, Genjuro appears to defend her whilst she transforms and leads the Noise away. Meanwhile, Hibiki encounters Miku and the okonomiyaki shop owner as they are trapped by an octopus-like Noise who detects noises. After apologising to Hibiki, Miku decides to lead the Noise away to give Hibiki a chance to transform, arriving just in time to defeat the Noise and save Miku. After Miku confesses the reason she was angry was because she was fearful for Hibiki's safety, the two make up with each other.

As Miku is allowed to join the second division, Genjuro goes to see Chris, explaining how he was to become her guardian after her parents died eight years ago, but she refuses his help. Having fully recovered from her injuries, Tsubasa is invited by Hibiki and Miku to spend the day together, where she comes to understand some of Kanade's words. Tsubasa decides to participate in a music festival taking place at the arena where that fateful incident took place. On the night of the concert, Hibiki decides to take on a Noise case on her own, where she teams up with Chris. Following the concert, Tsubasa decides to take on an overseas contract.

Ryoko is attacked by some American terrorists while hacking information off on Finé's computer, but she kills them using Black Arts, though takes some damage in doing so. As Chris and Genjuro come across the scene, Genjuro helps Chris understand what her parents fought for. As the Second Division investigates a clue given to them by Chris, Kadingir, a group of large airborne Noise appears over Tokyo Sky Tower, with Chris arriving to assist Hibiki and Tsubasa. Despite some hostility from Chris, Hibiki helps her and Tsubasa get along and together they defeat the Noise. Afterwards, however, Hibiki receives a distressing call from Miku that the academy is under Noise attack.

As Ogawa tries to get Miku to safety at the 2nd Division headquarters, they are attacked by Finé, who is revealed to be Ryoko as Genjuro arrives on the scene to fight against her. However, Ryoko manages to critically wound Genjuro and goes on to take the Durandal. As Ryoko goes on to confront Hibiki, Tsubasa, and Chris as they arrive on the scene, she explains how she is an ancient priestess who possessed Ryoko's body 12 years ago. She then proceeds to bring out the Kadingir, a huge cannon that she had been building in the 2nd Division's elevator shaft all this time, which she plans to use to destroy the moon which possesses some spell holding back her true power. As the cannon prepares to fire, Chris sings her Superb Song and sacrifices herself to stop the beam from completely destroying the moon, to the shock of Hibiki.

Shocked by Chris' supposed death, Hibiki goes berserk and loses control, attacking relentlessly at both Ryoko and Tsubasa. As Kadingir prepares to fire another shot at the moon, Tsubasa takes the full brunt of Hibiki's attack in order to hold her in place before standing to face Ryoko in order to try and launch a kamikaze attack which destroys Kadingir. As Ryoko turns her anger on Hibiki, who is not sure what to fight for anymore, the girl Hibiki had previously saved gives Miku the idea to, with the help of her friends, send Hibiki everyone's words of support. Upon hearing her classmates sing her school's anthem, Hibiki, along with Tsubasa and Kurisu who had survived, unleash the Symphogear's true potential.

As Ryoko summons an entire army of Noise, Hibiki, Tsubasa, and Chris work together to fight them off. Just then, Ryoko fuses herself with Durandal and the remaining Noise to become a powerful being. Working together, Tsubasa and Chris manage to retrieve Durandal from Ryoko and pass it on to Hibiki who manages to control its power thanks to Miku and the others and defeats Ryoko. Unwilling to listen to Hibiki's advice, Ryoko uses the last of her strength to pull the loose fragment of the moon towards the earth before fading away into dust. As Hibiki goes alone to stop the fragment using her Superb Song, Tsubasa and Chris join her and together they sing the ultimate Superb Song to destroy the fragment. Sometime later, as Miku finds herself cornered by Noise, Hibiki, Tsubasa, and Chris return safe and sound.