Heather Mason (Sharon) has a nightmare in which she runs from faceless men at a fairground. She hides in the merry go round as the faceless men gather round closer and closer. Pyramid Head is shown chained to the center, riding a bike contraption that causes the merry go round to go in circles. Men strapped as horses on the merry go round yell at heather. Alessa also appears, claiming that she cannot be beat and Heather must not come to Silent Hill. Heather is consumed by fire and her screams are heard in reality. Her father, Harry (Christopher) wakes her up and explains that it was just a nightmare and as soon as they make their new house feel like home, her dreams will return to normal, but she must promise to not ever go to Silent Hill. Harry is then killed from behind by a creature of Silent Hill, Heather screams and wakes up for real this time.
Heather draws something in her notebook, assumedly something about her dream. At breakfast, it is collected that they have changed their names, location/home, hair color, etc. many times in the past to enable them to keep running. Harry gives Heather her early birthday present, a white vest she had been looking at at the mall. She puts it on and heads for her first day of school. The rules are, she must go to school and come straight home so that she will be safe. While Heather is away her father looks at her drawing book, rips out the pages and puts them in a wooden box with a symbol carved on top. It is shown that he saves all of Heather's Silent Hill drawings in an envelope. He looks into the mirror and a flashback is shown. He speaks to Rose, Heather's mom and his wife, and it is shown that Rose and (Sharon) were once trapped in Silent Hill. Rose found a portal that only allowed one person to return to reality, she saved Sharon by passing her through the portal. Rose says shes trapped but there is nothing (Christopher) can do but he must protect Sharon now because they (Silent Hill) will come looking for her because they need her. The portal closes and Rose is gone but Sharon returns to Chris with no memory of what happened. He lies and tells her that she was in an accident and her mom is dead. A medallion of some sorts with a symbol (same symbol on the box) falls from Sharon's hand when her father holds her. The flashback ends. On her way to school, Heather comes near a homeless man, for a quick second he has no face and Heather, in fear, backs up and is almost hit by a car. A strange man approaches her, apologizing, he thinks he recognizes her but Heather waves him off and walks to the school bus. In class she is introduced as a new kid by the teacher. When a mean girl asks her if she gets all her clothes from goodwill and the teacher pushes her to talk about herself, Heather explains that she moves around a lot so no one should bother learning her name or anything about her because she definitely wont remember or care for them. Impressed, the teacher also introduces the second new student, Vincent Cooper, who jokingly says he cant top Heather's speech. In the crowded hallway, there's an announcement on the P.A. but it quickly turns to static. Confused, Heather looks up to find the hallway deserted and the dimmed lights flickering. She hears children chanting Burn the Witch! and looks inside the window of a classroom to find kids in a circle in an old fashioned classroom pushing a girl around (reference to the first Silent Hill movie). She steps away to look into another window, the children turn around to look at her. As she steps away again, a faint voice calls her real name Sharon Da Silva. The hallway turns into a hellish Silent Hill hallway. An armless creature begins his way towards her when suddenly Vincent comes up behind her, bringing her back to reality.
They both talk but she rejects rudely his offer of having some coffee together.
The same weirdo who talked to her at the bus stop is awaiting her. Heather walks back to school, bumping onto Vincent, who stares back at the man and Heather.
She phones Dad telling him about the strange man. They set out a date at Happy Burger at the mall. Back at home, somebody is trying to enter. Dad says he loves her but he's taken.
Heather waits and waits at the mall, sitting at a bench. He looks at a clown who's serving a birthday cake to a child called "Heather". The clown waves at her and happily dances around, while happy children are running and playing all over the place. When she sees "Happy birthday, Alessa" in a balloon everything becomes gory and terrifying. The strange man calls her Sharon and runs after her. The hamburgers they eat are being cut at the kitchen by a butcher (Jason Best) from a tortured man who's hanging down as cattle in the kitchen, and then they are fry-cooked by Sergey Shpakovsky. Heather can't talk to her father. The man runs after her and tells her that he's Douglas Cartland. He has been paid by the Order of Valtiel to find Sharon Da Silva. Heather/Sharon still thinks that they are being followed because the police accuses Harry of killing her mother, but Douglas tells her that she had been imprisoned in a place called Silent Hill. They want Heather back.
They are attacked by a monster (Chad Camilleri) with a blade as an arm and a strange head and he cuts some fingers from Douglas. They run into the lift and the monster jumps on top of it. The attacker takes Doughlas away, who wants to really help Heather. She enters the rubbish room where a cleaner scares her. She takes off her jacket. When she leaves the school, the police are there, taking away the body of Douglas. That bloodied coat will lead them to the culprit, says Detective Santini (Jefferson Brown), holding a photo caption of Heather. Vincent is one of the bystanders and asks her what she saw inside. Vincent and Heather walk together. Frantically, Heather tries to contact her father, who won't pick up his mobile phone. Vincent lends his coat to Heather, who's trembling with cold.
Heather looksat some priests waiting for her. Vincent can only see a jogger. In the bus, there's a strange man (Peter Schoelier) mumbling and trying to seduce her. The conversation moves to the unexisting different between fantasy and reality as Vicent's crazy father (Malcolm McDowell) Leonard used to say.
Back home, Dad is not there. Heather calls out for him, but only Vincent approaches her. They both see the huge writing on the wall "COME TO SILENT HILL". Heather can't call the police. Heather recognises the round symbol, and tells Vincent that Silent Hill is the place of her nightmare, where Harry told her never to go. They check on the box with Heather's cutouts; she can't remember clearly wheyn she was adopted, and they also find the pendant which used to be Heather's, but one side is missing. Heather's got a gun.
The police knock, possibly on a matter related to Cartland. Heather takes Vincent with her as she can't drive. The police busts the door open. They stare at the writing on the wall. To the enquire of Detective Cable (Milton Barnes), Santini says that Heather is a murder suspect.
Heather reads Harry's letter to Sharon. Harry tried to protect Heather/Sharon at all costs. He didn't kill a random thief that day; he was a member of the Order told to take Sharon to Silent Hill, where she should not EVER EVER go. The Order needs Heather, he doesn't know why. - Images in sepia of Harry taking away Heather's school file from Ipwich High School. Harry has written books and books about the monsters and Silent Hill along the years. The story is that the British built a colony prison in a hill which used to be a cemetery for Native Americans, called the place of Silent Spiritis. The Order of Valtial have been waiting for 100 years for a child to be born, who will be the vessel for their god, who in turn would create a new world. There's also a newspaper cutout with the news about a fire going underground the town of Silent Hill, in the old mines. The place had to be abandoned, and the mines are still burning. Harry thinks that the Order of Valial tried to kill the demon Alessa, trying to burn her, but Alessa took revenge and brought darkness to the town.
They arrive to the end of a road. Vincent insists on stopping. They arrive to Jack's, a derelict motel. Vincent advises not to go to Silent Hill. They hug each other. Heather dreams about Alessa invading the town with darkness. When she wakes up, she insists on going to Silent Hill. Vincent tells her not to do, because she belongs to the Order. She was born and raised in Silent Hill, but he was sent to the world to make sure she would come back with him. Vincent tells her that going back to the real world is possible for a short while, as long as there is a sacrifise and pain as price. He lifts up his shirt and he's been tattoed the sign of the order with a knife in his own flesh. Vincent tells her that they are taught that Alessa is keeping everybody in suffering and that Heather is part of that evil, but Vincent now believes that, if Heather is part of Alessa, she is actually the innocent part. In order to kill Alessa, she must be completed first; then the Order will be freed. Heather's father is kept alive in a Sanctuary under the city by Claudia Wolf (Carrie-Anne Moss), Vincent's mother. Heather is adamant to rescue Harry, and Vincent tells her that she will need the other half of the amulet.
Throughout all this conversation, lights are flickering in and out, showing that evil is approaching. Leonard Wolf, Vincent's father, has got the other half in the asylum. Vincent wants to help Heather and go with her. Lights go out because the darkness is approaching.
Walls start bleeding. Everything falls off. Behind, they can see the real scenery of terrifying Silent HIll. As Heather is part of Alessa, she can free the darkness in herself to enter the usually hidden realm. A monster takes Vincent but leaves Heather untouched - Heather needs to enter Silent Hill by her own volition. The darkness recedes and Heather wakes up in messy motel room No 10 in Silent Hill.
Smog and fallen ashes surround the road leading to Silent Hill. People stare at Heather from behind closed windows. Churchbells are heard. Tied to a stake, with a huge placard saying TRAITOR, it looks that is Vincent's destiny. Dahlia (Deborah Kara Unger) arrives from behind the pole, and tells Heather that she shold not be there, because she'll be used. Heather knows who she is: Alessa's mother, who allowed the townspeople to burn her daughter as a witch. She was deceived; she thought Alessa was special, and that they would help her. Heather thinks that they all got what they deserved. Alissa didn't die - she was badly hurt but with her rage, her powers increased. She took revenge on the town and put the good innocent part of her soul in an innocent newly-born baby and the baby was Sharon, says Dahlia. Sharon was at Toluca County Orphanage and was adopted by unaware parents - Harry and Rose. She can't save Harry without condemming herself.
Darkness arrives, everything seems to fly up and Heather runs. Inside is safer. There are broken dummies, including one which is alive, a young girl, who becomes a dummy and a girl (Rachel Sellan) who's about to become one. That girl is freed and says that the monster - a huge spider made of dummy parts - is approaching. The spider takes the head of the newly-transformed dummy, and includes it within itself. The head comes alive and screams. The spider finds them because the exit door is locked. It takes the other girl, who had lost herself in the woods, but Heather is able to leave.
Claudia says that darkness convinced Vincent, but he says that Claudia's darkness created Alessa. Harry is tied down to a sculpture of the faceless monster. Claudia says that Vincent, in his madness, succeeded, and that where her sister Christabella failed, she will succeed as well. Vincent is taken to the asylum, while Harry wakes up.
Heather finds the asylum and Leonard's medical file. He is in room 12, so she takes that key. Heather kills a monster who jumps on top of her. Heather finds the room. With her torchlight, she can see blind Leonard. He was chained by Claudia, her own daughter. Leonard looks like a monster himself anyway. Leonard laughs at the wailing sighs of Vincent. Leonard is an ongoing project, so he's not become a monster yet. He tells Heather to place the amulet in his hand, and she does, pointing his gun at him. Leonard recognises the seal which was used to take a child outside. The amulet unlocks the true nature of things. Leonard says that she has already found the other half, because it's hidden inside of him. He uses the half of the amulet to stab himself and rejoin the two pieces. Leonard can see and tries to kill Heather but she shoots him.
The newly-born monster frees himself and takes Heather with him, but she takes the whole amulet out and the monster becomes only dust and ashes.
Now she has the amulet whole again. She tries to talk to Alessa. Imprisoned men grab at her until the monster with the blade arm appears. He starts cutting arms with its axe. Heather crawls onto a hole.
This corridor leads to a torture chamber. Several nurses are holding clubs, axes, butcher knives... They are blind, so they only move when they listen to something. They kill the two nurses who took Vincent there. He can't free himself without making noise.
Heather appears. Vincent tells him that Harry is at the sanctuary under the fairground and that he can help her. She frees him and with noise, the nurses stab the air and them. The use the hospital bed as a shield. Heather can't understand how they can live like that, but Vincent says that it's all he's known in his life. Vincent still tries to convince her of leaving without her father. The fair starts working.
They hide from some soldiers of the order in gas masks. They don't breath air directly because they think it corrupts them. Vincent kisses Heather and lures them away. It's exactly as in her nightmares. A soldier appears but takes off his mask and dies. The merry-go-round is working, and tongues of fire surround Heather. Alessa appears, first a child, then a teenager.
Pyramid Head makes the merry-go-round move. Alessa says that each person has their personal nightmare in Silent Hill when Heather confronts her. Alessa tells Heather that she's not welcome. When Heather tells her to go to hell, Alessa says they're already there. They embrace each other, Alessa trying to kill Heather and Heather saying that she loves her regardless. They exchange looks until Alessa disappears in dust, Heather passes out and the merry-go-round stops.
Heather wakes up. A door opens. Sharon/Heather meets her father, still tied. Claudia tells that darkness has invaded her sanctuary. Claudia wants to kill Harry so that his blood will feed the new god which will be born from Heather. Claudia says they need Heather's body. Vincent is present throughout all this conversation, but he can't do anything to help Heather.
Heather offers the amulet to Claudia, saying that she wants to see what Claudia really is. When Claudia touches it, she shows herself to be a monster like any other of Alessa's servants. Claudia fights Pyramid Head. Heather and Vincent unty Harry while Pyramid Head kills Claudia's nightmarish figure.
The three of them, Vincent, Heather and Harry leave. Harry says he can't leave. Harry wants to rescue Rose. Heather did her task, and he must do his. Harry tells Vincent to take care of Heather. Harry goes back inside Silent Hill.
Both Heather and Vincent walk through a road. They thumb a lift from a lorry. The lorry driver is Travis Grady (Peter Outerbridge) and they finally leave Silent HIll.
The second afterwards they finally leave the town, three police cars and a prison bus enter the smog-filled town.