Two years ago, the activation of the experimental 7G network shattered reality across Japan. Civilization collapsed as the laws of physics broke down, cities became isolated pockets of distorted existence, and strange phenomena took root everywhere. In the small town of Agano, residents who pass the age of twenty-one transform into intelligent animals. Among the few unaffected are four high school students: the impulsive and athletic Shizuru Chikura, gentle peacemaker Nadeshiko Hoshi, energetic gyaru Reimi Kuga, and the withdrawn but brilliant Akira Shinonome.

Shizuru has spent the two years since the 7G Incident searching for her missing best friend, Yoka Nakatomi, with whom she had a falling out just before the catastrophe. When she discovers a newspaper wrapping used by a delivery service that shows Yoka alive in the distant metropolis of Ikebukuro, Shizuru resolves to find her. With no functional transportation and the landscape too warped and dangerous to cross on foot, she learns to operate an abandoned Seibu 2000 series passenger train from a strange conductor named Zenjiro, the only human adult left in Agano. The train, which the girls later name the Apogee, becomes their lifeline as they follow the Seibu Ikebukuro Line thirty stations toward their destination.

The journey unfolds as a surreal and unpredictable odyssey through Japans transformed landscape. Each station along the route presents its own bizarre reality shaped by the 7G network. At Higashi-Agano, the girls encounter a seemingly welcoming town that secretly tries to transform visitors into mushroom creatures. In other places, they find miniature military bases ruled by a dictator who shrunk an entire population, zombie armies led by a human queen who paints herself blue to belong with her undead family, and a cemetery where the dead have become Jizo statues. The group faces challenges that force them to confront not only the physical dangers of this broken world but also the fractures within their own friendships.

As the journey progresses, deeper mysteries unfold. The enigmatic Zenjiro communicates with the girls by tapping Morse code through the train tracks, holding a hidden grudge against the inventor of 7G. Yoka, the friend they seek, is not merely stranded in Ikebukuro but has become the Witch Queen of the city, her reality-altering powers manipulated by the insecure scientist Poison Pontaro, who created 7G and refuses to undo his mistake. The manga, told from Akira Shinonomes perspective, follows the groups battles against Pontaros forces including his crow-turned-human henchman and the cat-like Chaos, all while the distance between Shizuru and Yoka narrows both physically and emotionally.

Reaching Ikebukuro brings the final confrontation. Shizuru must reconcile with Yoka, apologizing for having dismissed her dream of becoming an astronomer years ago, and convince her to help undo the catastrophe. Pontaro is defeated, and the 7G network is deactivated, returning the world to a new normal though some changes remain permanent. The girls begin their return journey to Agano, their bonds strengthened and the Apogee carrying them home. The manga adaptation, illustrated by Torimura, ran for three volumes, covering the full story of the anime series from a distinct narrative angle.