Silent Hill: Cage of Cradle is a prequel to the first Silent Hill game, set in the fog-shrouded town shortly before the events of the original story. The narrative centers on Matthew, a young man who has recently arrived in Silent Hill in an attempt to rescue his girlfriend, nurse Lisa Garland, from the clutches of the town's sinister cult. Lisa works at Alchemilla Hospital, where she cares for Alessa Gillespie, a severely burned girl whose immense psychic trauma has begun to warp reality around her. As Cheryl, Alessa's separated half, draws near the town, Alessa's powers surge, causing the nightmare world known as the Otherworld to bleed into the waking town.

Matthew is pulled into the Otherworld, a realm of rust, blood, and grotesque manifestations of human guilt and suffering. There, he comes face‑to‑face with Valtiel, a mysterious and monstrous figure, during its birth. Matthew is killed by Valtiel, and soon after, Lisa also dies. Lisa's spirit becomes trapped in the Otherworld, with no memory of her death, setting the stage for her eventual encounter with Harry Mason in the opening scenes of the first Silent Hill game. The manga ends at the same moment the original game begins, with the town consumed by fog and darkness. Through this compact narrative, the story explores the doomed relationship between Matthew and Lisa, the nurse‑patient bond between Lisa and Alessa, and the tragic consequences of the cult's manipulation of Alessa's power.