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- The subway sequence echoes an early scene in the film Jacob's Ladder, right down to the name of the street the Jacob is trying to reach.
- Heather can use a lightsaber.
- The Book of Lost Memories spells out the true origin.
- There's a scene in the Dark Office Building where a lone wheelchair is visible from a great distance, illuminated by a single light. Word of God has confirmed this is a shout out to the memorably creepy "Hello...Gordon" scene from "Session 9".
- Solid Snake appears as the corpse in the wall of the construction site where you get the silencer. This isn't clear in-game but was confirmed by Konami.
- The Borley Haunted Mansion at the amusement park is almost certainly named after, well, the Borley haunted mansion, better known as the Borley Rectory, reputedly the most haunted house in England.
- Heather's Princess Heart outfit is a pastiche of Magical Girls in general, and Sailor Moon specifically. That's one Sexy Beam!
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