Mamori Tokonome, a girl who was diagnosed with an irregularity in her body, is captured by agents and taken to a remote island known as Mermaid. There, she is attacked by two girls named Miyasato and Kouzuki, the former being a Liberator who arouses the latter, an Exter, to transform her into a gun known as a Liberator Arm. Just then, another girl by the name of Mirei Shikishima arrives on the island, protecting Mamori by transforming her into a sword, allowing her to defeat Miyasato and Kouzuki and escape to the jungle. Arriving at a white castle, Mamori and Mirei are trapped in a colloseum, they are confronted by another Liberator, Saejima, who uses one of her masochistist slave girls to bring out a ball-and-chain Liberator Arm. Just as the two are cornered, Mirei once again uses arousal to transform Mamori into the sword Liberator Arm, allowing her to defeat Saejima in an instant.

Following their battle, Mamori and Mirei are restrained by two other Liberators. While Mirei is locked away in a disciplinary room, Mamori wakes up in the care of Kasumi Shigure, commander of the Welter, who explains that all the girls on the island are carriers of something called the Armed Virus, who are divided into Exters, who can transform into weapons, and Liberators, those who can wield them. Charlotte Scherzen, one of the Liberators from before, then informs Mamori that she is to undergo a wedding ceremony to find a suitable Liberator as a partner. As Mamori is arranged to be partnered with a trainer named Tomomi Nukui, Meifon Sakura, a girl who enjoys running bets on Liberator fights, follows order to set Mirei free, allowing her to come to Mamori's rescue. Undergoing a Drive once again, Mamori and Mirei escape to the beach, where they properly introduce themselves to each other.

Mamori and Mirei are picked up by Meifon, who takes them to a small town run by Torino Kazumi, who takes care of girls who don't want to or are unable to stay at Veste. Meanwhile, despite Kasumi's attempts to keep it a secret, Charlotte learns about Meifon repeatedly stealing supplies from Welter, commanding Kasumi to go and apprehend her. The next day, as Kasumi arrives in Torino Town to search for Meifon, Mirei offers to take responsibility for the theft and turn herself in. When Charlotte prepares to attack her, however, Mamori comes to Mirei's aid, helping her to fight back. Just as they are overwhelmed by Kasumi, who doesn't use an Arm to fight, they are aided by two women, Rain Hasumi and Lady J, who together form the duo of Lady Lady.

Surrounded by Welter soldiers, Rain kisses Mirei to transform into the Disarmment Buster Arm that forces Exters out of their weapon states, while Lady J uses her skills as a motorcycle to fight back Charlotte and Kasumi. Just then, Akira Hiiragi, Welter's governor and allegedly the only male on Mermaid, arrives to prove Mirei's innocence, having encountered Meifon earlier, and recalls the troops, much to Charlotte's ire. After Lady Lady take their leave, Mamori starts taking an interest in Akira, much to Mirei's dismay, while Akira tells Kasumi about his interest in Lady Lady, who function differently from the usual Liberator partnership. Later that night, Mamori follows a vision of Akira into the jungle, unaware that it is an illusion set by one of Charlotte's followers to try and put her in Arm form to kidnap her. However, Mirei arrives in the nick of time, managing to overcome her opponent's mental attacks and defeat her.

Mirei, Mamori, and Kasumi come across a girl named Nimi Minimi who, after running away from the castle when Charlotte tried to force her and her girlfriend Noe Oya into separate partnerships, somehow wound up in a giant form. Nimi is brought to Atelier Torino, where she manages to get along with everyone despite her gigantic form. The next day, as Nimi suddenly grows even larger, Mamori encourages her to go and see Noe and tell her how she feels. This naturally causes panic as she approaches the castle, with Kasumi's attempts to stop her only causing her to grow larger still. Before Charlotte can attack, Mirei and Mamori break Noe out of detention so that she can reach Nimi, allowing her to return to normal size. Akira then explains that the growth was a cause of Nimi's powers, which had simply taken a while to activate, allowing Nimi and Noe to remain partners with each other.

Meifon works with her partners in crime, Hyouko Yundou and Futaba Kirii, to steal more goods from Veste while also making money from gambling. Feeling she can make a killing from bets, Meifon arranges for Mirei to enter a beauty pageant being held at the Mermaid Festival. On the day of the festival, Charlotte gets chosen as the winner, with Meifon deducing that Hyouko and Futaba had switched out the ballots in order to kiss up to Charlotte. Discovering what had happened, Mirei and Mamori face off against Hyouko and Futaba's decoys, while Meifon uses her love of money to transform herself into an Arm to fight against the real thing, coming out victorious. With Hyouka and Futaba's crimes exposed, the pageant is revoked while Meifon delivers the prize to Mamori.

Stressed from work, Akira, who is revealed to be a woman, sneaks out to be spend some time with Torino, keeping her identity a secret from Mamori and Mirei. Spending the night in Mamori's room, she recalls how her mother arranged for her to act like a man upon arriving at Mermaid in order to stay safe. The next day, some rebellious girls take one of the Ritters hostage in the building where Akira is keeping her male clothes. As Charlotte and Kasumi argue over how to approach the situation, Mamori, Mirei, and Akira follow a secret passage into the building in order to rescue the hostage, only to fall into a trap laid out by the Ritter, who was sick of her current life. With Mirei knocked out, Mamori has Akira drive with her in order to stop the terrorists, briefly exposing her identity to Mirei before leaving the scene.

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.

Kasumi recalls how she and her partner Hibiki Kenjo, who has been in shock ever after being attacked on the island, was protected by Akira and made commander of Warter. With Akira's gender exposed, Charlotte, under Momoka's influence, declares herself the new governor, sending soldiers to capture the residents of Atelier Torino, while Momoka and her allies use a mysterious power to inspect people's bodies for something. As Mirei infiltrates Feste, having Mamori take Akira somewhere safe, she is attacked by Kasumi, who is forced to fight her upon learning that Hibiki is being held hostage by the Adel team. With Mirei having to use her Enhance ability to defend herself, Mamori manages to rescue Hibiki and reunite her with Kasumi. After Mamori joins Mirei to defeat the Adel using the Valkyrie Effect, they are attacked by Momoka.

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.