"Space Brothers #0" serves as a prequel to the main "Space Brothers" series, offering a deeper exploration of the formative years of the Mutta and Hibito Nanba brothers, whose shared dream of becoming astronauts drives the narrative. The story begins in 2006, focusing on Mutta, a 25-year-old automotive engineer, and Hibito, his younger brother, who is already on the path to becoming an astronaut. The series delves into their childhood, highlighting pivotal moments that shaped their aspirations, including a life-changing encounter with a UFO that solidified their desire to explore space.

Mutta, despite his intelligence and creativity, struggles with self-doubt and a series of professional setbacks, including losing his job. Hibito, on the other hand, demonstrates unwavering determination and secures a position at the Japan Aerospace Exploration Agency (JAXA). The narrative juxtaposes their contrasting journeys, emphasizing Mutta's internal conflict as he grapples with feelings of inadequacy while supporting his brother's success. The story also introduces key supporting characters, such as Serika Itou, a fellow JAXA candidate who becomes a source of inspiration for Mutta, and Sharon, a NASA astronaut who plays a pivotal role in Hibito's training.

The prequel provides context for the brothers' relationship, showcasing their bond and the challenges they face individually and together. It explores themes of perseverance, familial support, and the pursuit of dreams against societal and personal obstacles. By the end of "Space Brothers #0," the stage is set for the main series, with Mutta reigniting his childhood ambition and deciding to apply for JAXA's astronaut selection program, marking the beginning of his journey to catch up to Hibito and fulfill their shared dream of reaching the stars.