* WhatAnIdiot: Oh Jeff, just because you managed to chase away the killer, that doesn't mean ''you should go after him''.
* BreatherLevel: The Mesh. The monster never enters the city.
* EsotericHappyEnding: Almost every ending FMV except for [[spoiler: Kamiya's/Dark Messiah ending]].
* HellIsThatNoise: The monster makes some pretty weird sounds when it's nearby. Without Naomi, this is the only way to know where the monster is.
* ScrappyMechanic: The "Auto Map". It fills out the area you're in as you explorer it but doors doesn't appear on it. Sometimes you even have to walk up against a wall for it to "map" it.
* UnfortunateImplications: Naomi lampshades that she likes the player and even talks about possibly dating the player when they escape. She is ''17 years old''. Although the player's age is never told, it doesn't cause that big of an unfortunate implication.
* FridgeHorror: [[spoiler: Be chased through the underground by cultists and a monster, just to find out that you are the '''reason''' behind not only the '''train wreckage''', but also the '''kidnappings''' that have been going on. And why? Because you '''are''' the Dark Messiah.]]