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The story of Silent Hill 3 is set in the year 2000.

Seventeen years have passed since the events of the first game, and Heather Mason (the baby whom Alessa Gillespie gave to Harry Mason at the end of the first game) is now a teenager. It is revealed that Harry took Heather into his care to raise as his own daughter.

While running an errand for her father at the Central Square Shopping Center, Heather falls asleep inside Happy Burger and dreams about Silent Hill where she finds herself wandering through a nightmarish Lakeside Amusement Park. After fighting her way past several monsters, Heather walks along the roller coaster's tracks until she is struck down by the roller coaster.

After the roller coaster incident in her nightmare, Heather wakes up. She exits the burger joint and calls her father and lets him know that she is on her way home. Just as she is leaving, however, Heather encounters a detective named Douglas Cartland, who was hired by a cult known as the Order to find Heather. Heather, thinking of him as a stalker, ducks into the ladies' restroom; she jumps out the window, but her way out is blocked on both ends, forcing her to find another way through the mall. Inside the mall, Heather realizes that there are strange monsters lurking around. In a clothing store, Heather finds a handgun to defend herself with.

As Heather wanders through the mall, she encounters a barefoot woman dressed in all black with flowing blonde hair. She is the high priestess of the Order, Claudia Wolf, who has been searching for Heather, or rather, Alessa, for a long time. Claudia tells Heather that her talents are required and to: "Remember me, and your true self as well", and that she will lead them to Paradise "with bloodstained hands." Heather then comes down with a serious migraine as Claudia departs. When Heather enters an elevator, its descent causes a radio to drop from the ceiling, which emits static whenever monsters are nearby. The elevator doors open up, revealing a second, more sinister-looking elevator that indicates a crossover into another reality. After riding the second elevator down, Heather then finds herself inside an otherworld version of the mall. Even though she is frightened, she manages to make it back to the real world after a battle with split worm (from SH1) in the mall's depths.

Once everything is back to normal, Heather heads for the Hazel Street Station so that she may return home. However, Douglas stops her; Heather assumes that the private investigator is on Claudia's side, but he tells her that he was only hired to find her. Heather leaves the bewildered man alone and enters the subway. As with the mall, the subway is deserted, with the exception of the odd monsters. Heather even has a close call when she narrowly avoids being run over by a subway car. Heather takes the aforementioned subway to the underpass and fights her way through the sewer-like corridors until she reaches a construction site, which she uses to reach another building, the Hilltop Center, that is adjacent to the construction site through an open window.

It is inside Hilltop Center that, while inspecting a bathtub, Heather enters the nightmare world once again. She encounters a man named Vincent Smith, who is also a member of the Order with Claudia, but has different views on where the cult should go. After a brief conversation, she abandons him as well, voicing her beliefs that there is something wrong with him. When Heather reaches the exit, she finds Glutton blocking it; Heather finds scattered pages of a fairy tale which contains the words 'Tu Fui, Ego Eris' that makes the monster disappear. After getting rid of the monster, Heather is brought back to the normal world and escapes the Hilltop Center.

Upon arriving at her home in the Daisy Villa Apartments, Heather discovers the body of her father, Harry Mason, slumped in his chair, having been brutally murdered. Heather follows the blood trail to the apartment's rooftop where Claudia is waiting for her. Her explanation for Harry's murder is that some 17 years ago, he thwarted the cult's plans, and that killing Harry would fill Heather's heart full of hatred. Claudia merely tells her that she wasn't the one that killed him, only that she gave the order to her companion, a monster known as the 'Missionary'. Claudia then tells Heather that she will be waiting for her in Silent Hill and leaves.

After killing the monster, Heather finds Douglas inside the apartment. He helps her move Harry's body into his room, covered by a sheet with lilies. Heather pays her final respects to her father and decides to find Claudia and kill her in revenge, despite the fact that Douglas tells her revenge isn't the answer. Douglas offers to drive her to Silent Hill, which she reluctantly agrees to. Outside the apartment, Douglas hands Heather a map of Silent Hill - a gift from Vincent - and tells her that Vincent says to look for a man named Leonard Wolf (Claudia's father). He also gives her a notebook from her father, which acts as an explanation of Heather's past and as a final goodbye to her.

Heather and Douglas arrive in Silent Hill the following day; the town itself is deserted and covered by Fog World. They set up refuge in Jacks Inn and then split up; Heather heads for Brookhaven Hospital, while Douglas goes over to search Leonard Wolf's house.

Heather searches the hospital for clues to Claudia's whereabouts. Instead, among other things, Heather finds demonic nurses, some of which are armed with revolvers. She also finds out that one of the hospital's patients, Stanley Coleman, has an unhealthy obsession with her, and that Leonard is imprisoned within the hospital. Heather also comes across a startling discovery about herself long forgotten; she is, in fact, the reincarnation of Alessa Gillespie, as she has memories of Alessa's life previous to the fire.

Heather enters the nightmare realm once again and it is here that she encounters Leonard Wolf. Unfortunately, Leonard has degenerated into a monster and attacks Heather, who defeats him. Heather acquires the Seal of Metatron, a talisman which Leonard possessed, and the hospital becomes normal once again upon Leonard's demise. Heather returns to Jacks Inn to meet with Douglas. However, just before Heather returns, Claudia and Vincent have a conversation about the cult, as well as Leonard Wolf's abusiveness to Claudia, in their motel room.

Vincent is waiting for Heather when she returns to Jacks Inn, Claudia having already left. Heather asks him about Douglas' whereabouts and Vincent tells her that he left a message: "The church is on the other side of the lake." He also tells Heather that Claudia is inside the church, and that she must pass through Lakeside Amusement Park in order to reach her. Heather follows Vincent's advice, only to find that when she arrives at the park, she enters the nightmare world once again, realizing that it has now become her nightmare. Heather follows the path to the roller coaster, only this time around, with foreknowledge of what is going to occur, she manages to jump off the tracks just before the cars run her over.

In another part of the park, Claudia and Douglas are arguing; Douglas feels betrayed by Claudia, saying that while Claudia says that Heather was kidnapped and brainwashed, he feels that Heather is actually a normal girl. Claudia then explains that they need Heather back into the cult because God needs to be born and usher in a new "Paradise" -- an eternal world filled with no pain, hunger, sickness, old age, greed or war. Douglas then points out that a place without any worries or negative implications is not really a paradise, but rather, a stagnant world where nothing happens of any real value. Douglas sighs, saying that type of world would be pointless and boring and in response, Claudia tells Douglas that she pities him. Douglas then pulls out his gun and points it at her, and what happens afterwards remains a mystery.

After exploring the amusement park, Heather eventually runs into Douglas once again, however, he is unable to come with Heather due to his broken leg which is implied that Claudia intentionally broke it by using her power of psychokinesis. Douglas reveals that his son was shot robbing a bank, and talks more about his life. Heather promises to come back once she is done with things, and she comes to find herself in the same area of the amusement park where Harry was seventeen years earlier. On the carousel, Heather encounters her doppelgänger, the Memory of Alessa. The other Heather is bloodied and severely burned. After defeating her dark self, Heather reaches the entrance of the cult's church.

Heather encounters Claudia inside the chapel and Heather tells her that Alessa likes the world just the way it is (which may have actually been Alessa, or just Heather pretending to be as a way of manipulating Claudia). Claudia has a strong will and explains that there is too much suffering in the world and the God of her cult will change all that, although Heather explains that suffering is a fact of life and that you just have to face that reality. Heather suddenly feels pain as the "God" is close to being ready for birth and Claudia leaves.

While fighting her way through the corridors of the church, Heather encounters Vincent inside the library. He asks her about the Seal of Metatron, which Heather has in her possession. Vincent is relieved, as he believes it can be used as a weapon to defeat Claudia, whom Heather finally catches up to inside the cult's inner sanctum. Claudia wounds Vincent by stabbing him from behind, as he is faced at Heather, and Heather is somewhat taken aback by this action. After Claudia calms down, she resumes her usual composure and thanks Heather for making God feel hate and becoming closer to paradise. Heather then points out that a God who believes in hate can never create a perfect world. Claudia retaliates by saying that even a joyful world can be a cruel place and that in order to understand sympathy, one must understand pain and suffering. Vincent, still alive, desperately tells Claudia that Heather has the Seal of Metatron; Claudia then reveals that the Seal of Metatron is nothing but a useless trinket before stabbing Vincent in the heart, resulting in his death. Heather nearly succumbs to her rage, but finally gets herself under control.

The pendant Heather wears around her neck was a birthday gift from her father. Inside, it contains a small capsule of Aglaophotis, a liquid known for exorcising demons. Heather swallows it and vomits the bloody fetus of the God onto the floor. After taunting Claudia that "God didn't make it," Heather attempts to stomp on it with her boot but Claudia shoves her aside and picks up the repulsive creature.

After ingesting God herself, Claudia falls through a hole, and Heather jumps in after her. Inside the chamber, Claudia is dead, after giving birth to the monstrous God. Heather then discovers the God, which resembles a repulsive skeletal body, with a reptilian female face, which resembles Alessa's, and some sort of shroud provided by Valtiel. Due to Claudia, God has been reborn. Heather kills the God, thus finally avenging her father. Heather then collapses to the floor and mourns over her father's death.

Heather returns to the normal amusement park. While there she acts very strangely as she approaches Douglas. She wields a knife and seems unresponsive. She acts as if she is about to kill Douglas but then suddenly stops and tells him she was just playing a joke. Douglas makes a comment on how she has a twisted sense of humour. She then insists that Douglas call her Cheryl, which is the name her father, Harry, originally gave to her. Douglas then asks if she is also considering going back to her original black hair colour, to which she replies that blondes have more fun. The game closes with the credits rolling over a still-shot of Heather visiting Harry's grave.