In the not so distant future, mankind has advanced to a state where complete body transplants from flesh to machine is possible. This allows for great increases in both physical and cybernetic prowess and blurring the lines between the two worlds. However, criminals can also make full use of such technology, leading to new and sometimes, very dangerous crimes. In response to such innovative new methods, the Japanese Government has established Section 9, an independently operating police unit which deals with such highly sensitive crimes. Led by Daisuke Aramaki and Motoko Kusanagi, Section 9 deals with such crimes over the entire social spectrum, usually with success. However, when faced with a new A level hacker nicknamed "The Laughing Man," the team is thrown into a dangerous cat and mouse game, following the hacker's trail as it leaves its mark on Japan.

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.