In 1867, Jebediah Foster and Esther Munroe ride to Silent Hill from the Dakota Territory in order to start a better life together. Along the way, they encounter the postmaster of the town, Howard Blackwood, who is on his way to deliver letters in Shepherd's Glen. Esther explains to Howard that she is inheriting her uncle's property, the abandoned Munroe farm just outside of town, and Howard reveals that it could require some repairs. They part ways, and Jeb and Esther reach Silent Hill.
Jebediah and Esther are astounded by Silent Hill's beauty and excited for their new life. After settling in at their new house, Jeb heads outside to put his horse in the barn, where he finds a bottle of whiskey. The whiskey triggers a flashback: some time ago, Jeb received money a man named Grimes in return for murdering a group of people for unknown reasons, and celebrated the payment with a drink.
Esther suddenly screams from the house. Jeb runs inside and discovers a Cherokee woman, Inola, sitting on the floor with bleeding hands and a knife nearby. As Jeb looks for rags to stop the bleeding, Inola has a personal talk with Esther about her child and her relationship with Jebediah. When Jeb returns, Inola states that she suddenly has to leave and that her wounds are manageable. Jeb is still annoyed by Inola breaking and entering into their home, but an unnerved Esther begs him to let her go. As Inola exits, Jeb tells her to take the knife with her, but she replies that it doesn't belong to her; she was "just returnin' it." Before leaving, Inola calls Jeb by his old nickname: Hellrider.
Jebediah Foster sits in bed with Esther Munroe, worrying that with all the sins he has committed, it might be too late for him to start leading a good life. Esther reassures Jeb that things will turn out okay, then reveals herself as a macabre, skeletal creature. Jeb awakens from this nightmare.
In the morning, Jeb leaves to talk to the local sheriff about Inola. In town, Jeb runs into Howard Blackwood, who informs him that Sheriff Seth Creviston is currently at Toluca Prison, overseeing its conversion from a POW camp to a normal prison. Jeb briefly experiences déjà vu upon hearing Creviston's name.
While waiting for Creviston's return, Jeb goes to Leek's Tavern and meets the owner, Jonas Leek. Jonas's wife, Helene, comes in and behaves very seductively towards Jeb, emasculating and embarrassing an increasingly hostile Jonas. She acts as if she and Jeb are former lovers, and even calls him "Hellrider." Creviston suddenly enters and defuses the situation.
Meanwhile, back at the house, Esther sweeps on the porch as the creature from Jeb's nightmare watches nearby. Esther suddenly has a chilling vision of a young woman struggling to give birth while her mother tells her, "Hurry! They're coming!" Esther passes out.
Creviston assures Jeb that Inola is harmless. Jeb disagrees, showing him the knife that Inola left at the house. However, Creviston cryptically suggests that the knife really belongs to Jeb, and that he just forgot about it.
As Esther wakes up on the porch, Inola appears and helps her into the house. Esther tells her that Jeb went to report her to the sheriff, and worries what might happen if he comes back and sees Inola. Inola tells Esther to rest for the sake of her baby and, before leaving, remarks on the irony of a criminal like Jeb reporting to the sheriff.
Two weeks after Issue 2, while cutting firewood near the house, Jebediah flashes back to his "Hellrider" days. It turns out that he has met Jonas and Helene Leek before: Helene carried on an affair with Jeb, until one day Jonas came home and found the two. In a rage, Jonas took Jeb's knife and tried to stab him, but Jeb used Helene as a shield, killing her. He then shot Jonas dead, took back his knife, and left.
In the present, Jeb is interrupted by Howard, who is passing by on his mail run. The two converse, and Jeb confides his feeling that there's something abnormal about Silent Hill. Howard says the town has a way of reminding people of the past, and brings up the legend about this land being filled with spirits. Howard speaks vaguely of his own past, of the hardships he endured as a slave, and of how he has even killed in self-defense. Jeb then tells of his time as a murderous outlaw—which was mostly brought on by his drinking—and of how Esther nursed him and helped him leave that life behind. However, Jeb defends himself by revealing that many of his victims were Native Americans he had been hired to kill by aristocrats or government officials, and thus claims that they don't count. Before leaving, Howard ominously says that "it all counts."
On Sunday, Esther has a nightmare of the same woman urgently trying to birth her child with her mother's frantic assistance. After waking up, she and Jeb prepare to go to the town's church, which she wants to visit before the baby's arrival. Jeb notes her ill complexion and advises her to rest, but she insists that she needs to go.
At the service, Jeb sees Seth Creviston and has another flashback: he once stole a sheep from a farm and cooked it. Sheriff Creviston tried to arrest him, but Jeb used his knife to slash one of Creviston's eyes out. Perturbed, Jeb takes Esther and leaves the church. Riding back to the house, Jeb declares that he's done with this town.
As Esther enters the house, Jeb goes to the barn and begins drinking the whiskey, oblivious to the fact that the skeletal creature is watching him, its belly very pregnant.
Jebediah sits in the barn, drinking and contemplating his old knife. Esther suddenly goes into labor, even though it's too soon. Inola and the skeletal monster—Inola's daughter, Awinita—enter the room. They lay Esther on the floor and prepare to "assist" the delivery.
Jeb hears Esther scream, but Helene appears and tries to seduce him. Jeb kills her by sinking the knife into her chest—the same way the real Helene died. Jonas then appears and tries to kill Jeb for stealing his wife, but Jeb shatters an oil lantern on Jonas' head, setting him ablaze. The fire spreads to the house.
Esther realizes that the pregnant woman in her nightmares is Awinita, and Inola is the one telling her to hurry before "they" arrive. Now, Inola echoes those words to Esther and tells her to push.
Creviston stands in Jeb's way, telling him that this is not about Jeb or Esther—it's about the baby. In defiance, Jeb kills Creviston with an axe.
Meanwhile, Howard Blackwood senses what's happening and rides for the Munroe farm.
Under Inola's instruction, Awinita seemingly "merges" with Esther, causing their babies to become one.
Jeb enters the house, and a final flashback reveals his darkest sin: during his mission to kill the Cherokees, he found Inola and Awinita, the latter trying to give birth. Jeb took out his knife and killed the baby.
Esther delivers the baby, and Jeb tells Inola to take it and leave. He then cradles Esther, who appears to be dead.
Outside the burning house, Inola meets Howard and introduces the baby as her daughter, Awinita. Howard calmly inquires about the fire, and Inola replies that the spirits of Silent Hill are no longer silent, that the fires burn for them, and that "they've only just begun..."