This is a list of popular fan theories regarding the game's many characters and references. Please note that one of what follows is considered canon. Some of these also contain spoilers, so read at your own risk.
- Strangely, due to the fact that it is called 'CAT-DOS' and the computer in one of the Cat's rooms glow a similar shade of red, some assume that the Cat is the creator of the CAT-DOS and/or the house.
- This theory is mainly based on the fact that Specimen 2 is encountered around the same time as the romantic victims notes and that the note found before Specimen 2's introduction is written in a somewhat poetic fashion on the same paper texture used for the romantic victim's notes. It has been suggested that Specimen 2 may be the ghost of the romantic victim.
- This theory, however, may be wrong, as with the 4th of July update the player can find new romantic letters that confirm he is dead and hinted to be a ghost, wandering around the mansion harmlessly.
- Some believe Specimen 4 to be the ghost of Matsuri, rather than a girl who was murdered by her.
- However, the fact that it is mentioned in a note that Matsuri died from a ghost that eats children and the fact that Specimen 4 appears to eat the player when caught may disprove the fact that Specimen 4 is Matsuri, but instead that Matsuri was killed by Specimen 4.
- It should also be noted that update logs refer to Specimen 4 as "Ringu", though unofficially.
- It is very possible that Specimen 9 survived the encounter with the The Protagonist. As Specimen 9 had previously survived GL Labs attempt at destroying the creature, it makes sense that an axe would not be enough to eliminate it completely.
- Based on its surreal and dream-like aspects, it's been suggested that the events of Room 410 exist mainly in the protagonist's mind. The "Threshold of Consciousness" would suggest that the Cat is an illusion, at the very least. This can be slightly supported by the fact that Specimen 7 is effective against those with psychological and/or past trauma issues.
- Some believe the game could possibly be based on the story of the Winchester Mystery House.
- The Winchester Mystery House is a mansion in San Jose, California that was built by Sara Winchester. She believed that since her family had amassed their fortune from making the Winchester Repeating rifle, the spirits of all the people the rifles had killed were troubling her. In order to combat this, she had a mansion built to house both her family and the spirits. The massive house stretched across 6 acres of land and included 10,000 windows, 2,000 doors, 47 stairways, 47 fireplaces, 17 chimneys, 13 bathrooms, and six kitchens. Along with it's size, the house contains bizarre design choices, such as staircases going into the ceiling and hallways that lead to dead ends. Legend says there are nails only driven half-way into the walls, as workers immediately stopped once they heard Sara had died. The house is now a very popular tourist attraction and many people claim that the spirits (now including Sara herself) still haunt the house.
Good Game Ending (Spoilers)
- There is speculation that the Protagonist survives after appearing to have been crushed by the falling ceiling.
- When the player appears in front of Spooky after the battle, there is a large blood stain on the floor of the new room. However, the room's textures are completely different from those in the room of the final boss, so it is possible that the Protagonist's death was faked.