Mamori Tokonome watches in astonishment as two girls show off their intimate relationship. Little did she know that she had to establish a similar relationship with another girl, Mirei Shikishima, in order to fight for her life.

Mamori and Mirei defeat Saejima, but are taken into custody by Charlotte and Ange. Now Mamori must prepare for a mysterious ceremony known as the Wedding.

Mamori and Mirei escape from the clutches of Welter. They soon learn the nature of the militant female-only group, and also discover a small peaceful village that is free from its rule.

Charlotte, Kasumi, and the forces of Wärter move in to take Mirei into custody, but the mysterious duo known as Lady Lady intervene. An all-out fight is about to break loose, but is halted by yet another new participant.

Kasumi leaves the castle to investigate a strange Extar reading in the forest. There, she finds Mamori, Mirei, and a truly, tremendously buxom girl.

The Mermaid Festival is here! Meifeng must control the outcome of the Beauty Pageant to cash in on her illegal gambling scam, and she knows just the right person for shaking up the votes.

Akira leaves the castle to go on a secret mission. He meets Torino, and decides to spend the night outside of the castle. Meanwhile, a hostage situation takes place nearby.

Lady Lady are asked by Akira to investigate a location said to contain the secret of Mermaid, bringing Mamori, Mirei, and Meifon along with them. Uncovering a hidden cave, the girls find an underground construction plant, where they are attacked by an Artificial Arm that Mirei finds all too familiar. Unable to drive with Mamori following the ordeal of her attack, Mirei unleashes the true ability hidden in her body to fight the Arm, but is still overpowered by it. However, Mamori, determined to protect Mirei, brings out enhanced abilities of her own and transforms into an enhanced arm, allowing Mirei to defeat the Arm. As the girls manage to escape the facility as it is destroyed, another island, having detected the Valkyrie Effect coming from the battle, sends a girl named Momoka Sagara to Mermaid to investigate.

Momoka arrives on Mermaid under the guise of a new transfer, quickly demonstrating her Exter abilities and becoming a part of Charlotte's Adel team. Quickly deducing Akira's true gender, Momoka manipulates Charlotte into confronting Akira in a battle in order to expose the truth. Noticing something about Momoka's power, Akira brings out the full strength of her Artificial Arm, Sri, against Charlotte and Momoka and manages to defeat them. However, Momoka brings out her true power as a third generation Artificial Arm, overpowering Akira and exposing her gender to everyone and encouraging Charlotte to become Mermaid's new leader, after which Mamori and Mirei discover Atelier Torino in shambles.

With Akira removed from power, Charlotte names herself the new Gouvernour, and immediately begins ruling Mermaid with an iron fist. Momoka and the other mysterious intruders seem to be taking advantage of this for their own gains.

As Momoka, who were once a part of the same experiments as Mirei, prepares to attack, Lady Lady show up to fight against her, but find their attacks ineffective against her Soldier Arm. Momoka and her allies then kidnap Mamori, learning of the potential within her and deciding to keep her to herself. Meanwhile, Mamori recalls when she was in the same organization as Momoka, having been exiled after refusing to kill others and later sent to Mermaid due to possessing the Armed Virus. Blaming Mirei for everything bad that happened for her, Momoka prepares to use Mamori's body for her own gains. Mirei, joined by Lady Lady, head to Veste to rescue Mamori and the other captives, fighting her way past Charlotte before confronting Momoka, who plans to use Mamori's own form against her.

Mirei struggles to fight against Momoka as she wields Mamori against her, but is aided by Kasumi, who is finally joined in battle by Hibiki, as well as Lady Lady and Meifeng. However, Momoka uses Mamori's Valkyrie ability to absorb other girls into her arm and become stronger, overwhelming the others in a single shot and absorbing them. Inside the blade, as the captives are attacked by tentacles that draw the Armed Virus out of them, providing Momoka with enough power to even destroy a satellite, Mirei manages to break free and reunite with Mamori, freeing her from Momoka's control and releasing the others. Combining together into a perfect form, the Valkyrie Drive, Mirei and Mamori battle against Momoka as she combines with allies to transform into a giant robot. With support from all of her friends, Mirei manages to defeat Momoka, removing the Armed Virus from her and everyone else. As the residents of Mermaid are finally given the chance to return home to their families, Mirei and Mamori, along with Meifeng and Lady Lady, travel around the world in order to help others carrying with Armed Virus.