Story

At the beginning of the game, Heather awakens at a shopping mall. Before she can leave the mall, Douglas Cartland confronts her, claiming to have information about her birth. Heather evades him and discovers that the mall is mostly abandoned except for monsters. She encounters Claudia, who hints about Heather's fate. Heather finds herself in the Otherworld version of the mall —monster-filled and decaying— and is eventually transferred back to the original shopping mall where she encounters Douglas, who confesses that Claudia had hired him to find her.
Heather leaves the mall and resolves to take the subway home. Having arrived at her residence, Heather discovers that her father has been killed by a monster under Claudia's orders, who tells her that she will be waiting for her in Silent Hill and leaves. Heather resolves to go to Silent Hill, intent on killing Claudia. She meets with Douglas in her apartment and accepts his offer to drive her there.
On the journey there, Douglas explains that Vincent left him a message, telling them to look for a man named Leonard, whilst Heather reads a memo left by her father before his death, which reveals that she is the baby girl that was left to her adoptive father, Harry Mason, at the conclusion of the first game, after he defeated the god birthed by Alessa Gillespie. Claudia seeks Heather to birth the cult's god, since Heather is Alessa's reincarnation.
Upon arriving in Silent Hill, which is abandoned and fog-shrouded, Heather checks Brookhaven Hospital for Leonard. After discovering that Leonard is Claudia's father, Heather meets a transfigured Leonard, who attacks her after discovering that she is not a cult member; Heather defeats him. She eventually meets Vincent, who directs her to a church via a local amusement park, purportedly at Douglas' request. Upon arriving at the amusement park, Heather is transferred to the Otherworld, where she finds Douglas wounded. She reaches the church and confronts Claudia, who kills Vincent. After swallowing a substance within a pendant that her father had given her, Heather vomits out the deity in fetus form.
Claudia swallows the fetus and dies after birthing the deity; Heather then fights and defeats the god.

Endings

- The "Normal" ending, which is the only ending available on the first play-through of the game, sees Heather and Douglas survive.
- The "Possessed" ending sees Douglas having been killed by Heather.
- The "Revenge" ending, which is a joke ending accessible by performing certain in-game actions, sees Heather talking with Harry and UFOs blow up Silent Hill.