Journalist Hayato Mikogami arrives in his hometown and begins investigating the enigmatic Skull Man. However, he runs into his target sooner than expected.

Hayato, temporarily a murder suspect, is released from police custody due to his connections. His further investigations reveal a possible connection between the Skull Man and an arson case ten years ago.

Yui receives a threatening letter and later becomes the target of blackmail. Kiriko follows Yui and Sayoko to the theater. However, the real target of the Skull Man is Sayoko, who turns out to be a mutant.

A dead body hung from a railroad bridge makes Hayato investigate the legend of the Phantom Monorail. However, once on board, he becomes the target of the Skull Man.

Usami, the Skull Man impostor, tries to eliminate the original. Meanwhile, Kiriko discovers a person from her past among the Byakureikai members.

Hayato and Kiriko run across yet another Skull Man killing the town mayor. With other trails getting cold, the two decide to investigate the Byakureikai from the inside.

Hayato and Kiriko are discovered and kicked out of Byakureikai, but Hayato discovers that one of the disciples there is an old acquaintance of Kiriko and the reason for her entering the town.

Hayato and Kiriko hide out in the woods, since Hayato is now a wanted criminal now. It is finally announced that Father Kanzaki is the Skull man, and with his Lost Numbers he would fight the new enemy cyborgs.