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Note: Revelation is set in January 2011.

The film opens with a nightmare; a teenage girl, Heather Mason, is running away from people in strange, ceremonial black cloaks in Lakeside Amusement Park. She then encounters a dark doppelgänger of herself who sets her on fire on a carousel. As she is engulfed in flames, she suddenly wakes up in a panic. Her father, Christopher Da Silva, comforts her, but is soon stabbed through the chest and killed by a monster with discs in its head, known as the Missionary. Heather then awakens again, and realizes that she was still dreaming. She has been suffering nightmares that have been growing increasingly intense.

The next morning, it is revealed that Heather is an older Sharon Da Silva, and that both Sharon and Chris have adopted new aliases: Harry and Heather Mason, in order to hide from the Order of Valtiel, the cult of Silent Hill, West Virginia. Chris has given Sharon strict orders to never visit Silent Hill. It is also revealed that Rose Da Silva is still trapped in Silent Hill, and in order to free her adopted daughter from the realm of the town, Rose located the Seal of Metatron — although in order to do so, she sacrificed herself. In doing this, Sharon lost many of her memories, including the events that transpired in the first film. Instead, in order to keep his adopted daughter safe and give her a normal life, Chris has told Sharon that Rose died in a car crash, and that her nightmares are simply dreams and not anything to worry about. It is the eve before Heather's eighteenth birthday, and Chris gives her a white vest as a present. Heather is slightly disturbed by it, considering it is identical to the vest she wore in her nightmare. The two embrace, and Heather leaves for her first day at a new school.

On the way to school, Heather has a vision of a homeless man turning into a monster and is startled. She is then confronted by a detective named Douglas Cartland who claims that she looks familiar. Heather refuses to speak with him. During class, she reveals that she's been moving from town to town and school to school for the past 6 years, and refuses to befriend any of the other students, claiming that it wouldn't matter. As she is walking to another class, Heather hallucinates a girl being teased by classmates. She then shortly enters the Otherworld version of the school and is approached by an armless monster. Heather is snapped out of the trance when she runs into Vincent Cooper, who is also a new student at the school, but she rebuffs his friendly advances.

Heather sees Douglas watching her as she leaves school and flees from him. She goes to Happy Burger in Central Square Shopping Center to meet safely with Chris, but he doesn't arrive and she becomes impatient. Heather has more hallucinations, including children eating flesh burgers and a man being skinned alive to produce meat. Douglas catches up to Heather and tells her that the Order is looking for her, and that he wants to help her. He reveals that the reason why Heather has been moving so much is not because her father murdered someone years before, but because the man Chris killed in Portland was a member of the Order who was trying to abduct Heather. Before he can tell her anything else, the Missionary arrives and assaults them. They try to get away through the elevator, but Douglas is pulled away and killed by the Missionary.

Heather leaves the mall, which has become a crime scene due to Douglas's death, but she leaves her jacket behind, causing the police to suspect she was responsible for Douglas's murder. Heather walks home with Vincent, only to discover that Chris has been kidnapped and a note beckoning her to Silent Hill has been left on the wall in blood. Heather retrieves a box containing the Seal of Metatron from her father's bedroom, although it is missing its other half, along with various documents regarding the mythology of Silent Hill. Police arrive at Heather's door, believing that she was responsible for Douglas's murder. Despite Vincent not wanting her to go, he gives in and drives her to Silent Hill.

On the way to the town, Heather reads Chris's research on Silent Hill and the Order along with a personal note to her from her father, and learns that she is an incarnation of Alessa Gillespie, who was burned alive with the knowledge that she would survive the fire. The Order intended to use the hatred she formed from her pain to perform a ritual to impregnate her with their god, but Alessa proved more powerful than they had thought, and she instead split her soul and dragged the cult into an alternate reality.

Heather and Vincent rest at Jacks Inn, where Vincent reveals that he is worried for Heather. As Heather sleeps, she dreams of Alessa wreaking havoc throughout Silent Hill, turning residents into ash and making the world peel away beneath her feet. Heather awakens and is told by Vincent that he is a member of the Order who was born and raised in Silent Hill's alternate reality. Although Vincent was taught to hate Heather his entire life, he reveals that he has fallen in love with her in the few hours since he met her at the school. He warns her to stay away from Silent Hill, but Heather causes the inn to shift to the Otherworld due to her sudden shock and hatred towards Vincent and his lies. Vincent is then kidnapped by the Missionary and Heather is knocked unconscious. When she wakes, she finds herself in the Fog World.

She enters Silent Hill and meets Dahlia Gillespie, Alessa's mother. Dahlia tells Heather that she is the manifestation of the good side of Alessa's soul, and that Alessa's rage controls Silent Hill. Heather tries to get Dahlia to tell her where Christopher is, but the sirens that denote the Otherworld shift go off and Dahlia urges Heather to take shelter and run as the world peels away around them. She runs into a room filled with mannequins and watches in horror as a woman is transformed into a mannequin. Heather then meets Suki, a young woman who was dragged into the Otherworld when she got lost in Silent Hill. Heather tries to save Suki from a mannequin-like monster, but Suki is dragged away and killed.

Heather then goes to Brookhaven Asylum, where she meets Leonard Wolf, the grandfather of Vincent and the former leader of the Order. Leonard tells Heather that the Seal of Metatron reveals the "true nature of things" and that he has the other half, and shifts into a monster after shoving Heather's half of the Seal into his chest. Heather is able to remove the Seal from Leonard's body, killing him, and she goes to locate Vincent. Before finding him, she is attacked by prisoners in the asylum, but her yells for help bring the attention of Red Pyramid, who rushes to her aid and chops off the prisoners' arms. Heather then finds Vincent in a room full of demonic nurses, who have just finished killing two members of the Order. She saves him, under the condition that he helps her find Chris, and the two go to Lakeside Amusement Park to find Chris. Vincent notes that the Otherworld has lasted unusually long due to Heather's presence in Silent Hill.

At the park, Vincent kisses Heather and then distracts the Brethren, a sect of the Order, to allow Heather time to get away. Heather makes her way to the carousel, where fire ignites in a circle, killing dozens of cult members of both the Brethren and the Order that surround her. Red Pyramid spins the carousel and it descends into the Sanctuary. As it descends, Heather meets Dark Alessa, the manifestation of the dark side of Alessa's soul. Dark Alessa morphs into an older version of herself; a ghostly version of Heather. She tells Heather that they are one and reveals herself to be a demon because she is the darkness of Alessa's soul. Heather and Alessa embrace in a "war of will-power," each pushing to overcome the other's will, but Heather finally "absorbs" her adversary, making herself a complete incarnation of Alessa and overcoming the darkness within her.

Heather finds the Sanctuary beneath the amusement park, and tries to free her father. There, she is confronted by Claudia Wolf, a priestess of the Order and the mother of Vincent. Heather gives Claudia the Seal of Metatron, recalling what Leonard told her about the object's power to expose one's true self. Claudia transforms into the Missionary — at this point, it becomes clear that Claudia was the being who murdered Douglas and kidnapped Vincent in Jacks Inn. When Claudia attacks Heather, Red Pyramid, as Alessa's "guardian and executioner," goes to Heather's defense. As the two monsters brawl, Heather frees Vincent and Chris. Although Red Pyramid gets injured, he succeeds in killing Claudia. Vincent, Chris, and Heather escape.

Upon returning to the entrance of Silent Hill, Vincent notices that the ashes have stopped falling, and Heather speculates that things will change, though Chris corrects her, claiming that it is still a town of lost souls. Chris, Vincent and Heather leave Silent Hill together, but Chris stops and turns back, saying that he must find Rose. He then disappears into the fog which disappears along with him, and Heather and Vincent return to reality. They hitchhike with a truck driver named Travis Grady. They drive away, only for a police convoy and a prison bus to head in the direction of Silent Hill moments later, with fog overcoming the road.