Three months following the battle with Finé, Hibiki and Chris work together to fight off the Noise and protect a transport carrying the Solomon's Cane, which scientist Dr. Ver believes could hold the key to fighting the Noise. However, before they can leave to see Tsubasa's concert alongside diva Maria Cadenzavna Eve, the base they are delivering it to is attacked by the Noise, with Dr. Ver and Solomon's Cane going missing. As the concert reaches its climax, Maria suddenly summons a group of Noise, holding the audience hostage and using the worldwide broadcast to prevent Tsubasa from using her Symphogear. Maria then reveals she possesses a Black Gungnir Symphogear armor, proclaiming herself and her group to be the successors of Finé.

After giving the world leaders 24 hours to relinquish their territory, Maria decides to release the hostages so she can fight against Tsubasa, preventing her from escaping to where she can safely transform. Just as Tsubasa is knocked towards a group of Noise, Shinji manages to shut down the cameras in time, allowing Tsubasa to activate her Symphogear and fight back. Before Tsubasa can get the upper hand on Maria, two more Symphogear users, Shirabe Tsukuyomi and Kirika Akatsuki arrive on the scene, with Hibiki & Chris arriving shortly after to back Tsubasa up. The head of Maria's operations, Professor Nastassja, sends in a giant regenerating Noise to allow Maria's team to retreat. To prevent it from escaping and endangering the public, Hibiki, Tsubasa, & Chris combine their Superb Songs to expose its core, allowing Hibiki to destroy it. After the battle, Hibiki feels hurt by Shirabe claiming her ideals are merely the words of a hypocrite, bringing up some traumatic memories of her past.

A week following the incident, and Hibiki is still concerned over what Shirabe said whilst Tsubasa and Chris, who had enrolled into the academy, help with preparations for an upcoming school festival. Later that night, Hibiki, Tsubasa and Chris are sent to infiltrate an abandoned hospital filled with Noise, affected by a gas that decreases their sync with the Symphogears. Dr. Ver soon appears, revealing he stole Solomon's Cane for himself and is working with the enemy. As Chris starts to become affected by the feedback on her Symphogear's attacks, Ver plans to unleash an experimental new creature known as a Nephilim onto the city, forcing Tsubasa to chase after it. Before Tsubasa can destroy the Nephilim, Maria appears before her once again, with Ver announcing her to be the reincarnation of Finé.

Tsubasa engages in battle with Maria whilst Shirabe and Kirika arrive to fight off Hibiki and Chris whilst they retrieve Ver. Nastassja soon arrives and assists Maria and the others in their retreat, taking Ver and the Nephilim with them and evading pursuit using stealth technology. The next day, as the festival gets under the way and Hibiki and Miku watch their friends perform, Shirabe and Kirika are sent on a mission to infiltrate the school and steal the Symphogear pendants to use as food for the Nephilim. Meanwhile, Chris is dragged in by her new classmates to perform for a karaoke contest, where she finds herself having fun. After her performance, however, Shirabe and Kirika reveal themselves and prepare to challenge her.

As Shirabe and Kirika decide to enter the karaoke contest themselves, singing one of ZweiWing's songs so that they can win Chris' pendant, armed forces approach a warhouse where Maria and Nastassja are hiding, but are confronted by Ver and his Noise army. Maria breaks down when she sees Ver mercilessly kill a group of children who happened to stumble upon the base, prompting Nastassja to have Shirabe and Kirika retreat before they can be declared winners. Hibiki, Tsubasa and Chris briefly catch up to them, questioning why they fight when they seem to enjoy singing, to which they say they will settle things in a duel. they are called to HQ where it is revealed Hibiki and Maria's Gungnirs share the same ressonance pattern. Meanwhile, Nastassja recalls how Maria's sister, Serena, had used her Swan Song to stop a rampaging Nephilim prototype, ending her life in the process. Later that day, the girls head to the former site of Kadingir for their arranged duel, only to find Ver, who states that the moon will fall towards Earth once more before sending the Nephilim to attack them. Hibiki fights against the Nephilim but becomes distracted by Ver's words, leading to her arm being bitten off by the Nephilim.

The Nephilim evolves from the energy gathered from Hibiki's arm, but Hibiki enters her berserk state again, regenerating her arm in the process, and rips out the Nephilim's heart before completely annihilating it. As Hibiki undergoes recovery, she recalls how she was unfairly treated like a murderer by her old classmates due to being the only survivor of the ZweiWing incident. Meanwhile, Tsubasa learns from Genjuro that Hibiki's constant use of Gungnir is causing it to spread across her body, fearing that it may end up killing her, or otherwise leaving her inhuman. Keeping this a secret from Hibiki, Tsubasa tells her that she shouldn't use her Symphogear again, using the berserk state as an excuse. Elsewhere, as Nastassja's illness starts to develop, Shirabe and Kirika search for Ver, who find's the Nephilim's heart and attacks near the school, prompting Hibiki to go into action.

Feeling more powerful than usual, Hibiki fights through Ver's defenses, only to be stopped by Shirabe and Kirika. As Hibiki suddenly feels a pain in her chest, Ver injects them with an overdose of LiNKER so they can use their Superb Songs against Hibiki. In order to stop them from dying the same way Kanade did, Hibiki uses her own Superb Song to cancel theirs out, firing off their excess energy into the sky. Shirabe and Kirika retreat with Ver to treat Nastassja, wondering why Hibiki protected them, Tsubasa arrives on the scene to stop Hibiki from overheating. As Ver reveals his plan to use the Nephilim's heart with the ShenshouJing relic they had retrieved, Genjuro informs Chris and Miku about Hibiki's condition, asking Miku to keep Hibiki from fighting so it doesn't spread further. Coming to understand Maria's kind heart, Nastassja informs her that she no longer has to play the role of Finé. Elsewhere, Kirika ends up protecting Shirabe from some falling pipes with a strange power.

It is revealed that Nastassja has merely told Maria to play the role of Finé's successor in order to gain Ver's co-operation. As Kirika starts to realise the cause of her new power, that she herself is Finé's vessel, Hibiki is informed of her condition and is told to take things easy until they can find a cure. Meanwhile, Nastassja's group use their relics to try and unleash something known as Frontier, only for it to fail to Ver's dismay, as they lack sufficient power. The next day, as Hibiki and Miku go to the Sky Tower, Nastassja and Maria also go there to negotiate with some US government agents, which is interrupted when Ver sends Noise after them just as they turn on them. As Maria makes her escape, fighting through both Noise and army soldiers, Hibiki and Miku work to help evacuate some of the citizens, which leads to Hibiki being knocked off the building. Activating her Symphogear to break her fall, Hibiki is shocked to see an explosion where Miku was standing.

As Tsubasa and Chris arrive to finish off the Noise, Hibiki falls into depression, believing Miku to have been killed. Meanwhile, Maria reveals to the others that she is not Finé, whilst still stating her desire to cooperate with Ver. The next day, Genjuro reveals they have found a GPS left behind by Miku, revealing she had survived the explosion, as she was rescued by Maria and is currently being held on their ship. Thankful that Miku is still alive, Hibiki and the others train their bodies with Genjuro. The next day as the Noise launch an attack on an aircraft carrier, Shirabe, not wanting Maria to suffer from seeing more people die, decides to fight against them. However, Ver instructs Kirika to inject Shirabe with Anti-Linker to knock her out of her Symphogear state. However, just as Tsubasa and Chris arrive on the scene, Ver reveals his latest experiment, in which Miku has been made into a Symphogear user.

Miku, who was experimented on by Ver with Linker to make her compatible with the Shenshoujing relic, battles against Chris, initially taking the brunt of her attacks before unleashing a powerful laser, forcing Chris to block against it to protect Shirabe before Tsubasa gets them to safety. As HQ takes Shirabe into custody whilst Chris fights against the Noise, Kirika stands in Tsubasa's way, leading Hibiki to confront Miku herself. Miku states she desired the Symphogear's power to keep Hibiki from fighting, but Hibiki states it isn't worth having a world without Miku in it and transforms to fight against her, given under three minutes before she overheats. Despite the Gungnir relic spreading through her body, Hibiki keeps fighting to reach Miku's humanity, taking the brunt of an attack with FIS uses to unleash Frontier. As an ancient civilization rises from the ground, Chris suddenly shoots Tsubasa.

As Miku makes a full recovery, it is revealed the blast she and Hibiki took both freed Miku from her mind control and cured Hibiki's condition. Meanwhile, Chris joins the FIS as they explore Frontier, which Ver powers up using the Nephilim heart. Injecting himself with Linker, Ver activates the Frontier, using the moon itself to pull it out of the sea, before destroying many fleets with its gravitational power. With the moon brought even closer to Earth, Ver reveals to Maria that his vision of saving mankind is to destroy all humanity and repopulate the Earth himself, leaving Maria devastated. As Tsubasa heads off towards Frontier, Hibiki encourages Shirabe to do what she thinks is right and go as well, hitching a ride with her. Arriving at Frontier, Tsubasa soon comes up against Chris as Shirabe goes up against Kirika, whilst Hibiki pushes ahead to find Maria, who is informed by Nastassja that her song may be able to stop the moon from falling.

Maria broadcasts her song across the world whilst Tsubasa, noticing a collar on Chris' neck, encourages her to give everything she's got. Meanwhile, Kirika and Shirabe's battle escalates to the point of using their Superb Songs, where it is discovered that Shirabe also possesses Finé's power. Feeling guilty, Kirika attempts to kill herself, but Shirabe takes the hit. Chris, freed from her explosive collar thanks to Tsubasa, appears before Ver demanding Solomon's Cane, countering his Anti-LiNKER by bursting out of her gear, before she is rescued by Tsubasa, recovering the cane in the process. In her consciencse, Shirabe is approached by the soul of Finé who, having taken Hibiki's words to heart, saves her life so that she and Kirika can help save Maria. Back in the control center, Ver launches the dome where Nastassja is towards the moon, but Hibiki stops Maria from killing Ver, instead taking on the power of Maria's Gungnir relic, reviving her Symphogear.

As Ver escapes and starts bringing Frontier up towards space, Genjuro pursues him whilst Hibiki joins Tsubasa and Chris to search for the Nephilim heart powering Frontier, coming up against a giant Nephilim Ver sends after them. Meanwhile, Maria is greeted by the spirit of Serena, who sings alongside her and the world, providing Nastassja with the energy she needs to put the moon back into orbit. As Shirabe and Kirika join Hibiki and the others in fighting the Nephilim, Maria uses the relic Serena left behind to combine the power of everyone's song and defeat the Nephilim. His plans failed, Ver attempts to overload the Nephilim heart, unleashing its true form, which can absorb the power of Symphogears. Using Solomon's Cane, the girls open a gate to the Noise's dimension, pusing the Nephilim inside it, entering the dimension themselves when Maria is dragged inside too. After combining their power to break through the Nephilim and return to Earth, Miku manages to seal the gate before the Nephilim explodes, taking out all of the Noise inside the dimension. With the world safe again, Maria expresses her gratitude towards Hibiki, letting her keep the Gungnir relic.