The story begins here on the shores of the vast blue sea, in Kamogawa, a provincial city of Chiba Prefecture, Japan. Madoka Kyono lives a busy life as the proud, and only, member of the Kamogawa Girls' High School Jersey Club, a school club dedicated to helping those in need. When a mysterious girl named Lan shows interest in joining the Jersey Club, Madoka is at first thrilled at the thought of having a new club member.

Madoka's excitement over her triumphant victory is short-lived when she is told by Pharos officials to be ready for the next battle. Feeling like she's been tricked into becoming a Vox pilot, a furious Madoka plans an escape. However, upon seeing Lan tormented by the guilt of getting her involved, Madoka has a change of heart and agrees to fight in the Vox.

Madoka regains her will to fight thanks to Yoko, but quickly finds herself outnumbered by the enemy Ovid. Lan, still wracked with guilt over getting Madoka involved in battle, storms out in Vox Rympha to help her comrade. But Lan's fear toward the Vox prevents her from bringing out the full potential of Rympha, which the enemy takes advantage of.

A new girl transfers to Madoka's school, introducing herself as Muginami. Recognising the girl as the one who previously infiltrated Pharos headquarters, Lan decides to keep a close watch on her. But Madoka, impressed by Muginami's abilities and free-spirited personality, decides to scout her into the Jersey Club instead.

Lan, still suspicious of Muginami's true objective, confronts her for some answers. To Lan's surprise, Muginami has the Memoria for the last remaining Vox, making her its pilot. To make matters worse, Muginami reveals that her 'brother' is about to arrive in Kamogawa, spelling great disaster for the city.

Lan tells the Pharos crew of Villagiulio's intent to destroy them as well as the Vox. Pharos stands by ready for the coming attack, while Madoka and Lan are both determined to defeat Villagiulio and have him pay for what he did to Muginami.