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 users 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.

As Hibiki tries to reason with Carol, refusing to don her Symphogear, Chris comes into contact with another Autoscorer, Leiur Darahim. When a second enemy attacks, Chris is able to escape harm thanks to a girl named Elfnein, who reveals she comes from a world of alchemy. Meanwhile, Carol tells Hibiki that destroying the world is task given to her before retreating, leaving Hibiki shocked with thoughts of her own father before passing out. Meanwhile, as Tsubasa and Maria attempt to flee from Phara, Maria suspects that Tsubasa is the one being targeted, lamenting how she herself has been forced by the government to pretend to be an agent. Both Tsubasa and Chris are soon put into a pinch when their opponents summon Alca-Noise, a new breed of Noise that has the power to destroy their Symphogear armor.

With Tsubasa and Chris' Symphogear destroyed by the Alca-Noise, Shirabe and Kirika, despite being hindered by being unable to use LiNKER, step in to help Chris and Elfnein escape safely while the enemy dolls, having completed their mission, retreat. Later, after Tsubasa and Maria return to Japan, Elfnein explains Carol's motives to the others, presenting them with a relic known as the Dwerg Dain. The next day, as Hibiki and her friends are confronted by the third Autoscorer, Galie Tuman, who summons more Alca-Noise, Hibiki, who had been conflicted about using Gungnir to fight, suddenly finds herself unable to sing the chant needed to transform.

As Hibiki and her friends are forced to flee, Maria arrives and uses Hibiki's relic to fight off the Alca-Noise with her Black Gungnir armor. Galie fights back, but Maria loses sync with the relic before she can destroy it, retreating instead. Wanting Hibiki to be able to sing again, Miku takes her on a walk to try to help her remember the reason she sings, only to come under attack by the fourth Autoscorer, Micha Jawkan. Pushed into a corner, Miku reminds Hibiki of all the people she saved with her power, giving her the resolve to transform once more. However, she is caught off guard by Galie's illusions and is dealt a critical blow to her relic by Micha. Determined to save Hibiki, Tsubasa and Chris prepare to go along with Elfnein's plan to counter the Alca-Noise; Project Ignite.

A week later, as Hibiki is still in a coma following her battle with Micha, Elfnein works on upgrading the relics with her Project Ignite, briefly experiencing some of Carol's memories of her father. When Alca-Noise start attacking generators in an attempt to cut off the base's power supply, Shirabe and Kirika steal some LiNKER and go into battle in order to buy Elfnein some time, coming up against Micha in the process. As both Shirabe and Kirika's relics are destroyed by Micha and her Alca-Noise, they are saved by the arrival of Tsubasa and Chris wielding their new and improved Symphogear armor.

Using their enhanced Symphogears, Tsubasa and Chris manage to withstand the effects of the Alca-Noise. Just then, Carol appears, using the Faust Robe of Daurdabla relic to transform into an adult form which uses her own memories as fuel for her power. Pushed by Carol's attacks, Tsubasa and Chris activate their relics' Ignite Module, in which they must fight their own impulses in order control the raw power previously seen in Hibiki's beserk form. As the two struggle to face their own burdens and regrets, they manage to snap each other out of it before they lose control. With her relic repaired, Hibiki joins the others and encourages them to try the Ignite Module once more, this time managing to overcome it and enter new forms that have the power to fight back against Carol. Having burned up the memories of her own motivation, Carol taunts Hibiki about her own cursed memory before using a capsule to burn herself to ashes.

After Maria, Shirabe, and Kirika's relics are repaired by Elfnein, everyone is sent on a training camp at the beach in order to master the upgraded Symphogear. Just as they are enjoying themselves, they come under attack by Galie, who appears to be acting without Carol's orders. Determined to prove her strength, Maria attempts to activate the Ignite Module against her, but ends up going berserk instead and winds up losing. Lamenting her defeat, Maria spends time with Elfnein, where they are once again confronted by Galie, with Phara using the distraction to sneak into their base to obtain some data. With Elfnein echoing her own advice to stay true to herself, Maria finds strength in accepting her own weakness and overcomes the Ignite Module, using her new form to defeat Galie. Later that night, as Hibiki and Miku make a run to the convenience store, Hibiki is shocked to see her father is one of the clerks.

Hibiki meets up with her father but refuses to hear him out, feeling he hasn't changed since the day he left her family amidst all the harrassment she faced following the ZweiWing incident. Joining Shirabe and Kirika on a mission to defeat some Alca-Noise attacking some underground conduits, Hibiki's anger towards both her father and herself puts her at a disadvantage against Micha, prompting Shirabe to step in to protect her and Kirika. As Shirabe and Kirika end up arguing with each other following the incident, Genjurou determines Micha's purpose was to download conduit route data to locate hidden entrances. Later, Leiur attacks the HQ while Micha targets Shirabe and Kirika, who learn that the reason they were arguing was because they didn't want to become a burden to each other. Realizing that people get mad at them because they care, the two activate their Ignite Modules and combine their strengths to defeat Micha. Meanwhile, Carol reawakens in a spare body, able to see what the enemy is doing through Elfnein's eyes.

Learning that the Autoscorers may be targeting two locations at once, Chris, Shirabe, and Kirika go to the Undersea Dragon's Palace, where many relics are sealed, while Tsubasa goes with Maria to her family's mansion, where she is met with disdain from her father, Yatsuhiro. Tsubasa soon comes up against Phara, who overwhelms her with her ability to destroy anything defined as a sword before destroying her family's keystone. Afterwards, Tsubasa explains how the decisions of her grandfather, revealed to be her biological father, left her in a poor relationship with Yatsuhiro. When Phara attacks again later that night, she receives encouragement from Yatsuhiro to focus on her own dreams, showing that he had always cared for his daughter, allowing her to overcome her own definition as a sword and defeat Phara. Meanwhile, Chris' team confront Carol and Leiur to stop them stealing a relic, only to suddenly come up against Dr. Ver.

With Shirabe and Kirika unable to bring themselves to attack Ver, since he is the only one who can produce LiNKER, Chris is scolded for using her ability recklessly in trying to stop them. Meanwhile, Carol reveals to HQ that she had been using Elfnein as a mole without her knowing, while Tsubasa and Maria learn from Phara that Carol's plan is to make the wielders use Ignite Modules on the Autoscorers. Unaware of any of this, Chris, reminded of the warmth she had been seeking by Shirabe and Kirika, activates her Ignite Module and works with the others to fight back against Leiur, after which they retreat back to HQ and prepare to fight against Leiur's giant form.

Chris manages to destroy Leiur while Elfnein gets injured protecting one of the staff from the damage caused by her attacks on HQ. Meanwhile, Hibiki meets up with her father again, telling him he needs to be the one to take the first step in getting their family back together. Just then, Carol's Chateau appears in the sky, powered by both the cursed melodies gathered by the Autoscorers and the assistance of Ver. After deeming Ver of no further use and seemingly dispatching him, Carol turns her attention towards Hibiki, knocking away her relic. While seemingly running away in fear at first, Hibiki's father manages to distract Carol long enough to retrieve Hibiki's relic, helping Hibiki realise that he had always been protecting her in her own way. Hibiki is soon joined by the other wielders as they get her father to safety and once again confront Carol, as she uses her relic's Burst Mode to resonate with the Chateau as it spreads a photosphere across the entire planet. While Hibiki, Tsubasa, and Chris fight against Carol, Maria, Shirabe, and Kirika head inside the Chateau to try and shut it down, where they suddenly find themselves in the presence of Nastassja.

Believing miracles were the thing that condemned her father to death, Carol spreads Alca-Noise across the city, the Symphogear wielders, sensing that Carol is feeling alone, fight against them. Just then, Carol prepares her ultimate weapon, a giant metal beast, but Hibiki, supported by her friends and her Armed Gear, powers through to defeat it. Just as the beast is about to explode into a miniature sun, Hibiki reaches out to save Carol, who finally remembers her father's goal; to help people understand each other. Three days later, as Carol's whereabouts remain unknown, Hibiki laments over not being able to do much for Elfnein's declining condition, but Miku gives her some support. Later that night, Elfnein is approached by Carol, who appears to have lost all of her memories, stating her desire to live and merging with Carol to become one. Afterwards, Hibiki rekindles her relationship with her father and helps their family reunite, while Elfnein becomes a member of S.O.N.G., who analyze the data left behind by Ver.