Going off of data retrieved from Tiki's remains, the Symphogear users head to Antarctica, where they are confronted by a powerful automated "coffin" that Adam was investigating. Despite the overwhelming odds, Hibiki and the others manage to destroy the coffin, inside of which they find the corpse of a Custodian.

On the way back from Antarctica, a remnant alchemist of the Bavarian Illuminati, Elza, attempts to retrieve the Custodian's corpse, but is forced to retreat by Shirabe and Kirika. Later, as Tsubasa becomes too worried about the attack to focus on her concert, Maria gives her some encouragement and ends up performing with her during the concert. However, another alchemist, Millaarc, sends Alca-Noise to attack the concert, slaughtering practically everyone in attendance and placing a seal on Tsubasa, who is left emotionally devastated. Meanwhile, as the corpse is analysed by the Americans, it turns into dust when the bracelet on its wrist is scanned.

Hibiki and Chris are sent into action after Elza and Millaarc attempt to silence a delinquent that witnessed a deal between them and some men in suits. Retrieving a briefcase filled with a rare type of blood that was dropped by Elza, S.O.N.G. deduce from the delinquent's account that an organization is helping the alchemists. Shortly after awakening from her ordeal, Tsubasa is further shaken from harsh words from Fudou, who states she isn't strong enough to protect people. Later that night, Kirika and Shirabe confront Millaarc after she targets a hospital for more blood, but she escapes thanks to Vanessa, the third alchemist of their group known as Noble Red. Afterwards, it is revealed that Vanessa, who now possesses the Bracelet of Shem-Ha found on the corpse, is working together with Fudou.

As Fudou and Noble Red attempt to activate the Bracelet of Shem-Ha, one of suited men before, who is about to be killed for his failure, attempts to use it for himself, only to be destroyed by it. With their hideout destroyed by the resulting explosion, Vanessa distracts Hibiki and Maria to help the others escape to a new location, revealing that she and others want to regain their human bodies. Discovering that Vanessa was planted with a tracking device during the battle, Noble Red lures the Symphogear wielders inside a labyrinth to attack them from all sides. However, Hibiki is aided by the spirit of Saint-Germain inside of her and granted a new power known as Amalgam. Just as Hibiki gains the upper hand and tries to reach out to Vanessa, S.O.N.G. is raided by the Japanese government, who demand that they abort their mission.

Citing Hibiki's Amalgam as an unknown weapon, the supposed inspector from the Japanese government commences an inspection of S.O.N.G. HQ, forcing the wielders to take some days off. Meanwhile, it is revealed that Fudou convinced Noble Red to aid his plan in exchange for the blood they need to survive after they escaped the Bavarian Illuminati. As Hibiki and Miku invite Tsubasa and Elfnein to join them on their day off, Miku lashes out at Hibiki for not being considerate of Tsubasa's feelings. Just then, an Alca-Noise attack occurs nearby, with an illusional effect that Millaarc cast on Tsubasa during their last battle causing her to envision the enemy as Millaarc and go berserk in her attacks. Meanwhile, the real Millaarc uses the battle as a distraction to chase down Miku and Elfnein.

Miku and Elfnein are kidnapped by Noble Red and brought to the Chateau du Triffages to further their plans, involving both the Bracelet and a mysterious device. Meanwhile, as the wielders learn that Miku is a potential vessel for a god, Vanessa targets Shinji in order to retrieve some evidence that would link them back to their hideout. As Maria and Chris are sent to stop her, a golden light shines from the castle, where the mysterious Shem-Ha emerges.

After Millaarc attempts to use mind control to have Elfnein activate the Chateau, the bracelet goes out of control and spawns Shem-Ha, who proves too powerful for Hibiki to defeat. Retreating to base, the gang learn that the waveform used by the creature is similar to a song Maria used to sing. Back at the Chateau, Elfnein's plea for help causes the Autoscorers, whose spare bodies were chained to the reactor, to reactivate and come to her aid. As the Autoscorers are all defeated trying to hold off Noble Red until reinforcements arrive, Elfnein manages to call upon Carol's powers to defend herself.

Reawakening inside Elfnein's body, Carol manages to fend off Noble Red and get in touch with SONG, instructing them to deal with Shem-Ha while she tries to rescue Miku. As the wielders struggle to utilize their phonic gain without Hibiki, Noble Red attempt a second attack on Carol by trapping her in the labyrinth, but Carol uses up her power to both break out of the labyrinth and provide the others with the phonic gain they need. Returning to the fray, Hibiki is aided by the others and uses Amalgam to break her way inside through Shem-Ha's attack, only discover that they have taken over Miku's body.

Just as Miku tries to resist Shem-Ha's control, Fudou uses the seal placed on Tsubasa by Millarc to have her turn against the others and bring Miku to him as part of his plan. Joining a raid of the Kazanari household, Maria clashes off against Tsubasa, managing to slap some sense into her and break the seal on her. Fudou attempts to shoot Tsubasa for disobeying him, only for Yatsuhiro to sacrifice himself protecting her. Meanwhile, Noble Red, who were betrayed by Fudou, attempt to steal Miku to use Shem-Ha's power for their own gain, only for Miku to cut them down and break free. Standing against Fudou, Tsubasa manages to get approval to us Amalgam to overpower him, but Genjurou steps in to prevent her from killing him. At the moment, a device activates on the Moon.

Maria attempts to take on Shem-Ha, only to discover she has revived Noble Red as more complete monsters and recruited them to her side, forcing Maria to retreat while Shem-Ha rises a tower known as Yggdrasil. Fudou was apprehended and awaiting trial for his crimes, cursing Genjurou that songs cannot save the world and the Power of God unifies humanity. With a research team scheduled to be sent to the moon to investigate lunar ruins that are reacting to Yggdrasil, the wielders are tasked with protecting the rocket from Noble Red, who have become more powerful due to Shem-Ha's improvements. Although the rocket is destroyed, Kirika and Shirabe use their Amalgams to overpower Elsa before Tsubasa allows the wielders to hijack Noble Red's teleportation spell, sending them to the lunar ruins.

Both the wielders and Noble Red are spread across the lunar base Marduk, having to deal with its automated defenses. Meanwhile, Maria's relic leads her and Tsubasa to Marduk's core, whether they speak with an operating system based on the mind of Enki. Enki reveals that Shem-Ha had instilled herself as a data fragment in all human beings, forcing him to seal her using the Curse of Balal, which Shem-Ha now seeks to destroy in order to control all of humanity with Yggdrasil. Tsubasa and Maria are confronted by Millaarc, who uses a clone of herself to fight against them, but the two use their unified songs and Amalgams to defeat her. Back on Earth, however, Yggdrasil towers start raising all over the planet.

Despite Elfnein and Carol's attempt to stop her, Shem-Ha begins using the world's computer networks to have Yggdrasil cover the entire globe in a barrier. Back on the moon, Hibiki and Chris face off against Vanessa, ultimately saving her and the others from being sucked into space. However, Shem-Ha takes control of Vanessa and uses her to install a virus in the Marduk's network in order to destroy it, forcing Noble Red to use the last of their strength to send the wielders back to Earth, resulting in their deaths similar to how Saint-Germain and her friends risked their lives to save the others. With humanity working together to hold back Shem-Ha's hacking attempt, the wielders activate their X-Drive in preparation for their final battle against Shem-Ha.

As Shem-Ha brings out her final form to fight the wielders, Carol burns up her memories to protect them from Shem-Ha's attack. Shem-Ha then begins using her bio-terminal network to take control of all of humanity, but Hibiki, fueled by determination to save Miku, manages to disrupt Shem-Ha's power and finally drive her out of Miku's body. With Yggdrasil still active, Miku dons the Shenshōjing Faust Robe and joins the others in a united Superb Song, allowing them to simultaneously destroy all the Yggdrasil cores around the world. With the world restored to normal, Hibiki and Miku tell each other their true feelings.