Flesh Rots. Blood Corrupts. To Be the Ultimate Anti-Hero… You Have to Be Bad to the Bone! Otomo City: where freedom and justice have atrophied to the bone; where conspiracy rules the day and death stalks the night… Death in the form of the Skull Man, a literal Grim Reaper whose skeletal grin presages grisly mayhem and murder, even to the monstrous mutants that haunt the city’s underworlds! Now, to investigate a bizarre slaying, journalist Minagami Hayato and photographer Kiriko Mamiya must stalk this ultimate predator, through a festering cadaver of a city where the corruption flows in rivers as deep and foul as the sins of the reigning elite, and unearth a secret so shocking that an entire city has been turned into a tomb to contain! In a nightmarish necropolis where nothing is as it seems, vengeance comes in the form of a living Death’s-Head in SKULL MAN!
When a young actress becomes the latest victim in a string of suspicious murders, journalist Hayato Minagami returns to Otomo City to see if there is any connection between the deaths and a local urban legend. Upon arrival, Hayato meets Kiriko Mamiya, an aspiring photographer, who attaches herself as his assistant. Hayato doesn't have long to wait to have his suspicions confirmed and becomes an eyewitness to another murder.
After collapsing outside of the apartment, Hayato is labeled as the prime suspect for the murder. Luckily, Hayato has friends in high places and is able to go free. With the authorities not believing his story, Hayato begins to search for answers on his own. The town is full of rumors, but are the recent strange events actually tied to a decade-old arson case?
The media goes wild when the actress Yui Onizuka receives a death note. After all, Yui has taken over the role vacated by her murdered friend Hitomi Tachibana. Blackmail seems to the motivation, but not everything is what it seems to be around Yui.
Hayato and Kiriko think they may have a new lead when a body is found at a railroad bridge. New talk erupts that this new murder may have a connection with the Phantom Monorail. However, chasing down this new urban legend will put Hayato on a collision course with the Skull Man.
The incident on the Monorail have the press and the cops on the hunt for the Skull Man. The ties between the Otomo Pharmaceutical labs, The White Bell Society and The Phantom in Black seem to be drawing tighter together, especially when a new victim is found.
Hayato and Kiriko infiltrate the Byakureikai by disguising themselves as members of the White Bell.
Kiriko finally finds the man that she has been searching for.
Nami's old boyfriend is back in town. Kiriko and Hayato investigate a clue they were given.
Something is going on with Nami's body.
An announcement is made that Father Kanzaki is really Skull Man and that he and the Lost Numbers are now going to fight the new cyborgs.
Detective Shinjou waits until the battle against Skull Man and the cyborgs is over before going to Father Kanzaki's church and try to find out more out Skull Man.
Hayato promises to return to town and stop Masaki Kuroshio.
Now that Masaki Kuroshio wants to create a new humanity, the Skull Man vowes he will stop him.