Arrested for reckless space driving and destroying a police drone, the super human Chiharu and her volatile cyborg childhood friend Makina find themselves facing community service. Due to prison overcrowding, they are assigned alongside four other recently detained misfits: the silent motorcycle gang leader Akane and her bumbling subordinate Kanata, as well as the cynical mercenaries Kurt and Max. Their sentence is a week of cleaning the Milky Subway, an aging interplanetary train docked for maintenance. What should have been a simple punishment takes a catastrophic turn when a miscommunication with the train’s faulty AI causes the old locomotive to suddenly launch into deep space with the six convicts still onboard.

The story unfolds largely through flashbacks as police parole officer Ryoko interrogates Chiharu about the incident that resulted in Makina being reduced to a disassembled state. As the train hurtles uncontrollably through the galaxy, the narrative cuts between the escalating crisis onboard and the events leading up to it. The group initially splinters along familiar lines, but the desperate situation forces them to work together. While attempting to reach the front carriage to regain control, they clash with malfunctioning security robots and navigate the labyrinthine interior of the train, gradually uncovering its mysterious and slightly ominous history.

The central characters are defined by their contrasting backgrounds and personalities. Chiharu is cheerful and easygoing but dangerously passive, a trait that has enabled Makina's violent behavior. Makina is a hot-headed full-conversion cyborg whose face is a digital screen, and she relies on a suite of built-in weapons to solve problems. Their unlikely allies include Akane, a quiet but fiercely protective super human, and her aggressive but physically hapless companion Kanata. Rounding out the group are Kurt and Max, a pair of cyborgs who are surprisingly competent but demand payment for any assistance. The series is set in a retro-futuristic galaxy where 1980s aesthetics blend with advanced technology, creating a world of interplanetary highways and outdated train systems.

Over the course of twelve short episodes, the narrative follows the group's chaotic journey to stop the runaway train. Key arcs focus on the unlikely bonding between the characters, such as when a brawl between Makina and Akane abruptly ends upon discovering they share a passion for the same pop idol. Another significant thread explores the societal prejudice faced by cyborgs, revealed through the backstories of Kurt and Max, who left stable jobs due to discrimination. As the train barrels toward a potential intergalactic incident, the rag-tag team must learn to trust one another, leading to a climax that forces the impulsive Makina to confront the consequences of her actions.