|Murphy Pendleton, a convicted felon, is the protagonist of Silent Hill: Downpour. He has been incarcerated for several years at Ryall State Prison after stealing a police cruiser. Seeking revenge for unspecified reasons, Murphy strikes a deal with George Sewell, a corrections officer at Ryall, to secretly grant him access to a sequestered inmate, Patrick Napier, in the prison shower room. After reminding a confused Napier that they used to be neighbors, Murphy savagely beats him. The scene cuts to black before Murphy lands the finishing blow.
Sometime later, following a riot at Ryall, Murphy and a few other inmates are scheduled for transfer to Wayside Maximum Security Prison. They are accompanied on the transport bus by Anne Cunningham, a Wayside corrections officer who appears to have a particular interest in Murphy. The bus route passes just outside of eastern Silent Hill. Here, the road suddenly drops off into nothingness, forcing the driver to pull on the wheel, which sends the bus hurtling through the road barriers and down a hill.
Murphy regains consciousness in a forest next to the wrecked bus and decides to make a run for it. Anne finds him in the wilderness and attempts to apprehend him, but slips into a deep ravine, barely managing to hold on. Here, the player, as Murphy, can choose to either leave her or assist her. Despite the player's choice, she falls into the chasm.
Murphy continues on, winding up on the outskirts of Silent Hill, where he meets Howard Blackwood, an eerily calm mailman. During their brief, cryptic conversation, Howard tells Murphy that the roads are all out and that the best way to leave town is via the nearby sky-tram. Suddenly, Murphy glimpses a mysterious, wheelchair-bound creature in the window of a nearby house. Apparently not seeing the figure, Howard excuses himself to deliver the rest of his mail.
Somewhat confused, Murphy makes his way to the abandoned Devil's Pitstop diner. In the kitchen, Murphy discovers a gas leak and tries to turn it off, but accidentally starts a fire in the process. He activates the sprinklers to put out the fire, but as the sprinklers fill the room with water, the diner transforms into a water-filled hell. Exploring this new environment, Murphy encounters the Void, which rapidly sucks in everything around it. Realizing he can't fight the entity, Murphy flees and eventually finds himself back in the normal version of the diner.
Murphy surveys the area surrounding the diner and enters an abandoned house, finding another escaped prisoner, Sanchez, attacking what seems to be a helpless woman. Murphy intervenes, but the "woman" turns out to be a Screamer, which immediately kills Sanchez by slashing his throat. Murphy attacks the monster and defeats it. Although a little shaken, he cautiously explores further, eventually finding a change of clothes and a police badge. The badge is decorated with a black mourning band, indicating that its owner is dead. After changing out of his prison attire, Murphy plays the arcade-puzzle Jail Break and gets a ticket for the sky-tram, which takes him to the Devil's Pit gorge in southeastern Silent Hill.
There, Murphy meets John Sater, a depressed former tour guide for the Devil's Pit's various attractions and tours. JP tells Murphy of an old railcar train in the mines that can take him into the main town. In the caverns, Murphy discovers a newspaper article detailing a train accident in the Devil's Pit that resulted in the deaths of eight children, implicating JP's on-the-job drinking as the cause. Soon after, Murphy finds a suicidal JP hanging over a lookout rail, and the player is given the choice to either console him or taunt him. Again, despite the player's decision, JP jumps to his death. Murphy finds and powers up the railcar, but his ride through the mines turns into a hellish tour populated by monsters that try to kill him. The train derails, and Murphy loses consciousness.
Murphy awakens near an exit, but runs into a bloodied Anne, whose only concern appears to be apprehending him. Despite Murphy's pleas to cooperate, Anne remains resolute. While making the arrest, Anne inspects his person and finds the mourning badge. She quickly becomes distraught, apparently having known its previous owner. In a fit of rage, she nearly shoots Murphy, claiming that people like him do not deserve to live, but cannot bring herself to do it and collapses into tears instead. Anne tells him to leave her alone, to which Murphy reluctantly agrees.
Murphy wanders Silent Hill's main streets and encounters more of the town's creatures. When it begins raining, he takes refuge in the abandoned Hillside apartment building, where a nearby radio picks up broadcasts from DJ Bobby Ricks. Some of the broadcasts are song requests specifically made out to Murphy; others are quiet pleas for help from anyone who's listening. When the rain dies down, Murphy begins searching for Ricks and runs into Howard Blackwood. He tells Murphy that the radio station is located in the Centennial Building, before walking off again into the fog.
Murphy locates the building, and finds his parole papers attached to the entrance, which causes a flashback of Ryall Prison. Murphy and Sewell appear to be having a private conversation regarding their deal to murder Patrick Napier, the sequestered inmate from the opening scene. Officer Frank Coleridge, spots the two talking and calls Murphy over to hand him his files. Coleridge asks Murphy about the nature of his conversation with Sewell, but he dodges the question. Coleridge warns Murphy to use caution when dealing with Officer Sewell, as his deals tend to not work out so well for the other participants. It becomes clear that Coleridge has made a substantial effort to help Murphy receive an early release from Ryall because he believes that Murphy is a genuinely good person. Coleridge also says that he is confused as to why a smart man like Murphy would do something as reckless as stealing a police car for no reason. The flashback ends, and Murphy continues his search for DJ Ricks inside the building.
While ascending the floors of the Centennial Building, Murphy has another vision of Ryall Prison. In this vision, Murphy appears to be having a conversation with Officer Sewell in his office, having decided to go through with the plan to kill Patrick Napier. During their exchange, Sewell reviews the details of their agreement and ominously tells Murphy, "You owe me one." Sewell also implies that Murphy stole the police cruiser and got himself arrested on purpose in order to confront Patrick Napier in prison, but his reason why isn't divulged. Murphy leaves the room, and the vision dissipates.
Murphy finds Ricks, who initially behaves in an unusually casual manner, but soon begins speaking in hushed tones, as if somebody or something is listening in. Ricks reveals that he has been operating the radio station for a very long time, waiting for help. He tells Murphy of a boat docked at the marina, that they can both use to escape the town, but goes on to say that they must first find the boat's keys, which were apparently stolen by an intruder. When Murphy suggests hot-wiring the boat, Ricks says that it won't work, as the town has "rules" that must be adhered to. Before they can leave, Anne shows up, once again determined to arrest Murphy. However, as an apparent punishment for Ricks breaking the "rules," Screamers ambush the studio and kidnap both him and Anne. Murphy is left all alone, as the building shifts to a prison-like Otherworld. Murphy flees the Void, encounters the Wheelman again, and ends up falling off the exterior of the building's clock tower.
Waking up on a bench back in the "fog" world, Murphy once again meets Howard, who hands him a letter requesting his presence at St. Maria's Monastery. Confused and frustrated, Murphy refuses to accept the letter, but Howard explains that it isn't about what he wants (suggesting that Howard knows more about the mysterious town than he initially let on). Given no other choice, Murphy accepts the letter and continues on. He passes through the stormy town and arrives at the broken-down monastery, where a nun cryptically tells him, "You were the only family we were able to locate." She asks Murphy to look around the place, and to come to the building's morgue whenever he's ready.
Murphy finds the monastery in a dilapidated state, and must take an alternate route to the morgue. On the way he encounters a small boy through the window of a locked door. The boy refuses to unlock the door because he believes that Murphy is the Bogeyman, as he's been told by an unnamed crying girl. The only way Murphy can prove he isn't the Bogeyman is by memorizing a poem that the children of the monastery's orphanage recite to make the Bogeyman disappear. As he treks through the monastery to gather the pieces of the poem, flashbacks reveal that Murphy's son Charlie was drowned in a lake a few years prior, which explains the recurrent theme of water in Murphy's Otherworld. At this point it has also become clear that Patrick Napier was the one responsible for his son's death -- which ultimately spawned Murphy's strong feelings of disdain for child molesters and murderers. In the present, Murphy returns to the locked door where he originally met the young boy. The real Bogeyman appears in the room and slowly approaches the boy. Murphy desperately struggles to recite the poem, but the Bogeyman kills the boy before he can complete it. The Bogeyman then drops the boy and places a finger to the mouth of his mask, shushing Murphy, as he concludes the poem.
The door unlocks and Murphy approaches the child's body, now in the form of his son Charlie. He mourns his death, but is interrupted by a young girl who accuses him of killing the boy/Charlie. She runs, and Murphy gives chase, scared that the Bogeyman will get her too. The monastery transforms into the Otherworld during the chase, forcing Murphy to dodge the Void and at one point even the Bogeyman himself. Eventually Murphy winds up in the morgue with the nun from the entrance standing next to a covered gurney. Murphy tells her that there has been a mistake, and that he buried his son years before. The nun replies that everyone grieves in their own way, and removes the sheet from the gurney, revealing a "dead" Bogeyman underneath. Angered, Murphy cries that the monster isn't his son; it's a murderer. But the nun insists that Murphy accept him as his own, calmly informing him of the perils of revenge and the path that Murphy has set himself upon by pursuing it. Murphy admits that what he did to Patrick Napier did not solve anything, but still attempts to rationalize his behavior. She simply says that the answers are right in front of him if he chooses to look.
Murphy notices a key with a silver keychain labeled "freedom" around the Bogeyman's neck, matching the description of Ricks' missing boat keys. The nun tells him that they are his if he wants them, but only if he accepts the Bogeyman as his own. Murphy takes the keys, but the Bogeyman springs to life and attacks Murphy. They are both transported to a forest area by a lakeshore, where they engage in battle. Murphy gains the upper hand and defeats the Bogeyman with its own hammer. He then finds himself back in the morgue with the Bogeyman dead and unmasked on the gurney, its face alternating between that of Murphy's and Napier's. Charlie appears and congratulates his father on defeating the Bogeyman. Having accepted that his past actions did nothing to assuage his guilt, Murphy tells his son that it doesn't matter and that it won't bring him back, to which Charlie comforts him by saying that it isn't his fault.
In a moment of clarity, Murphy apologizes to Napier (now in the form of the Bogeyman), and closes his eyelids. This causes the image to dissolve, leaving only the keys behind. Murphy runs his hand over the engraved word "freedom," before leaving the morgue. Now with the boat keys, Murphy makes his way out of the monastery through the sewers and arrives at the marina. He starts Ricks' boat and departs from Silent Hill, but Anne soon appears behind him holding a gun to his head, ordering him to turn the boat around and return to Silent Hill. She tells him that the town showed her things, that it knows her, and that the town won't release either of them until they settle their unfinished business. Murphy refuses to return, and tells her, "You may as well shoot me." Anne complies and pulls the trigger.
A flashback shows a meeting between Officer Sewell and Murphy back at the prison, sometime after Murphy's confrontation with Napier. Sewell reminds Murphy that he set up the meeting between him and Napier and looked the other way; and that it is now time for Murphy to return the favor. Sewell tells Murphy that his job is to kill an unnamed individual, assumed to be an inmate, who Sewell claims "deserves it." He then explains that there will be a riot at the prison that evening, allowing Murphy to slip away to the showers, where he will find this person.
Murphy wakes up inside a prison cell in Overlook Penitentiary, with the Wheelman sitting right outside the bars watching him. After a few seconds he wheels off and the doors open, allowing Murphy to explore the prison. He finds a note addressed to him, telling him to meet someone in the showers. Progressing through the prison and fighting enemies, Murphy eventually makes his way to the showers. Inside are four crime scene markers, indicating a pool of blood, a prison shank, the mourning police badge, and a bag of crime scene evidence. After examining all four, a voice calls out from behind him followed by the glow of a flashlight. Murphy approaches the light which shuts off as soon as he nears it, and blood begins seeping underneath the doors. Opening them, Murphy finds another shower section with a bagged body lying in the center of the floor.
As Murphy approaches the body, the world around him transitions to the Otherworld. Murphy races through it while avoiding enemies and the Void yet again. He eventually reaches a large door with two giant Scales of Justice hanging before it. Murphy places the prison shank, the bag of crime scene evidence, and the mourning badge on one scale and the doors open. Inside, surrounded by platforms and prison cells, is a much larger version of the Wheelman who has been haunting Murphy throughout the game. The monster quickly becomes hostile and Murphy must run around the room, pulling out the monster's giant life support tubes to defeat it.
After the Wheelman is defeated, Murphy finds himself back in the showers with the feeble version of the monster's body lying dead at his feet. Anne enters, and is horrified at what Murphy has done. Confused, Murphy looks down and finds in place of the Wheelman's body, the body of Frank Coleridge, the friendly police officer from Ryall who had persistently warned Murphy about socializing with Sewell. A flashback reveals that when Murphy made his way into the showers the night of the prison riot, armed with a prison shank hidden behind his back, Frank Coleridge was the one waiting for him. Coleridge tells a visibly distraught Murphy that Sewell was supposed to meet him there, before noticing that Murphy is concealing something behind his back. Unbeknownst to Murphy at this time, Officer Coleridge had agreed to submit testimony for an internal investigation of Officer Sewell, bearing witness to the illegal activities and transgressions Sewell had been conducting at Ryall, which would undoubtedly result in his arrest and subsequent incarceration. At this point, Sewell enters the room and tries to convince Murphy to kill Coleridge and uphold his end of the bargain, while Coleridge attempts to talk Murphy into dropping his weapon.
In the present, Anne reveals that Coleridge was her father. She tells Murphy that he was a good man and that she idolized him, even following in his footsteps to become a cop. After Frank Coleridge was attacked the night of the riot, he fell into a vegetative state; having to rely on a wheelchair and life support until the day he died. Anne is unaware of Sewell's involvement in her father's beating, so she tells Murphy that every time she looked at her father in his deteriorating physical state, she saw a monster: Murphy. Murphy then transforms into the Bogeyman before her as she describes how she had to pull strings, call in favors, and do "sick things" in order to have Murphy transferred to the prison where she worked, presumably so that she could kill him herself. After finishing her speech, Anne shoots Murphy, who then pursues her in his Bogeyman state.
Depending on whether the player survives this encounter or not, along with the moral choices they have made throughout the game and whether or not they decide to kill Anne or spare her, the conclusion of the battle and Murphy's fate varies.