Near the end of the game, the player will encounter areas identical to the end of Silent Hill. This includes camera positions, captions and even notepads (used as a save point in Silent Hill). These notepads have messages on them from Silent Hill's protagonist, Harry.
In response to the negative criticism over the new voice overs to the HD version of Silent Hill 3, Konami came out to the public, telling fans that the reason the original voices could not be used in the remastered version was that they were unable to get in contact with voice actress Heather Morris (who plays Heather in the game). However, in a recent interview with Morris, she revealed that Konami had never contacted her at all in the first place.
The game features numerous references to Silent Hill 2 (2001), including several small Silent Hill 2 posters in the Mall. When playing the game with a Silent Hill 2 save game content on the memory card or hard disk, other references will appear:
- In the Mall, you are given the option to retrieve something from a dirty toilet. When doing so, Heather will crouch and hesitantly move her hand towards the toilet, accompanied with suspenseful music. At the last moment she comes to her senses, turns to the camera and says "Gross. Who would do something like that anyway?". (In Silent Hill 2, the player had to retrieve a wallet from a clogged toilet).
- When examining your mailbox in the apartment building, Heather comments that there is no mail, not "even from a dead wife". Silent Hill 2 starts with the player receiving a letter from his wife who has been dead for 3 years.
- When examining the fence on the roof of Brookhaven Hospital, Heather says "it doesn't look like it's about to break". James from Silent Hill 2 was thrown through the fence off the roof.
Originally going to have a completely different story, but at the request of the fans, the story became a follow-up to the original Silent Hill.
When exploring the 'evil' version of the office building, the player will encounter a sheet of glass in a hallway. Behind the glass is a shot of a wheelchair in a beam of light - exactly like Session 9 (2001)'s movie poster.