In Silver Guardian, high school student and gamer Suigin Riku studies at the prestigious Shinryou Private Academy, a school built for the elite and the children of the wealthy. Suigin has none of that money or status; to cover his tuition, he works a string of part-time jobs and lives far below the world around him. During one such job, he dives into a pool to save his pet cat even though he cannot swim, and he is rescued by Rei Riku, the beautiful and popular daughter of a game developer. He quickly falls in love with her.
At the same time, Suigin is drawn to another girl he meets in Dungeon Century, his favorite online RPG. When the game is scheduled to shut down, he assumes the adventures they shared are over. But the day after the shutdown, he discovers that Rei and the girl from the game are one and the same. Soon after, Rei gives him a new game designed to replace Dungeon Century: Grave Buster, a tomb-raiding adventure. When Rei is suddenly kidnapped, Suigin is pulled inside Grave Buster and sets out to save her.
Gin no Guardian turns that rescue mission into a search for the secrets hidden inside the game, pushing Suigin deeper into a dangerous virtual world tied to Rei's fate.