A massive anomaly caused a great earthquake that ravaged Japan's mainland and destroyed most of Tokyo, sinking three-quarters of the city into the Pacific Ocean.

Ten years later, you, a seemingly ordinary ninth grader attending Nagano Prefecture's middle school who survived the great earthquake, leaving you with a normal life and no memories of the tragedy. This all changes when a mysterious person covered in blood and crimson armor floats through your classroom windows and massacres your entire class, but spares you and embeds a red crystal shard into your chest. Within days of the massacre, your placed on trial as a suspect. Due to evidence rigged against you, your sentenced to death at Deadman Wonderland, a prison that doubles as a theme park run by warden Tsunenaga Tamaki (who posed as your lawyer and was secretly responsible for the manipulated evidence).

At the prison, your fitted with a special collar that monitors his location and vital signs. A lethal poison is constantly injected into your bloodstream through the collar, but it can be neutralized by consuming a peculiar candy-like medicine every three days, which can be acquired through various activities in the prison, such as performing for audiences, working backstage, and purchasing with Cast Points (a form of currency among inmates at Deadman Wonderland). To gather Cast Points, an inmate must participate in the facility's lethal games and survive. Fortunately for you, your aided by a albino girl named Shiro, who appears to know you, and Yoh Takami, a fellow prisoner hoarding Cast Points to free his sister, who was imprisoned for murder after their mother neglected to protect her during the earthquake.

While trying to survive as an inmate on death row, you intends to find the "Red Man" to clear his name. In a bizarre twist, you develop the ability to manipulate your own blood.

You have become one of the prison's "Deadmen," an isolated group of prisoners possessing the Branches of Sin, the capability to control their blood.