Oftentimes, people are most vulnerable when they are lonely and unable to get along with those around them. Isolation is felt more keenly amongst a crowd, so some will try to find solace in the strangest of places, where the unknown lurks. Such people include Ayumu Aizawa, a former city boy now living in the countryside of Tana, and Kisa Tanigawa, a young girl who has a hard time relating to others. What these two share in common is a feeling that their life has gone astray. Zettai Shounen tells a story of strange phenomena affecting two different settings, with no explanations of their origin or sudden appearance. All that is known is that these phenomena seem to center on individuals with mixed emotions toward themselves and others.

In the distant future, trains are no longer bound by their physical tracks. Instead, they take to the skies and travel across the universe on the Galaxy Railways, transporting mankind from planet to planet. However, the Galaxy Railways are no safer than traditional trains: criminals, terrorists, and vile aliens always find a way to stir up trouble. Manabu Yuuki, a rash and hot-headed man, is the latest addition to the Galaxy Railways' elite Space Defence Force (SDF). These brave men and women are responsible for protecting the railways and responding to any unprecedented danger, risking their lives to protect the innocent from evil. But as this drama unfolds and the SDF's greatest crisis draws nearer, Manabu must truly learn what it means to be a member of the SDF before it is too late.