The live action special Skullman Prologue of Darkness serves as a prequel to the 2007 anime series and is also framed as a pseudo prequel to the larger Cyborg 009 universe. The story is set in the town of Otomo, where a journalist named Hayato Mikogami returns to investigate disturbing rumors of a series of brutal killings committed by a mysterious figure wearing a skull mask. He is soon joined by a young photographer named Kiriko Mamiya, and together they begin digging into the dark secrets hidden beneath the town's ordinary surface.

As Hayato and Kiriko investigate, they uncover a complex web of connections between the victims, a powerful local pharmaceutical company, and a mysterious new religious sect. Their search for the truth reveals a terrifying scientific conspiracy involving experiments that create strange, half-human, half-animal creatures that roam the streets at night, driven by a thirst for blood. The special also follows a separate narrative thread centered on a pharmaceutical researcher named Hiroshi, played by Shigeki Hosokawa, and his fiancée Michiko, played by pop singer Ami Suzuki, who become entangled in a mission to steal secret documents from a laboratory, leading to a fateful encounter with the masked skull man. This live action episode functions as an origin story for the Skullman, positioning the character as a dark prototype that precedes the creation of the cyborgs in the 009 universe.