* 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]].
* SpecialEffectFailure: No matter who your partner is, later on, you see a ghostly vision of Naomi in a field of sunflowers. The problem is, the sunflowers are a real life photograph (rather than any in-game rendering or pre-rendered background) ''and'' they are the ''exact same colour'' as the name text. Oops.
* ThatOneDisadvantage: Besides the game making you a OneHitPointWonder, if you lose a companion, and choose to not recruit another one, you're doing this trope on purpose. Some companions has a few disadvantages, which can make you easier to get killed or cornered: Naomi can't doing anything, besides serving as a radar [[spoiler:(until later)]], Ivanoff and Kamiya can stun the monster, but lacks Naomi's radar [[spoiler:(and the latter locks you into a bad ending)]], and Rene has limited stuns, and the same disadvantage as Ivanoff and Kamiya.
* 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.
** Varying on your experience with the game, many mechanics in the game:
*** The companion mechanic: With one, you can survive a hit, but you lose said companion.
*** Keeping Naomi alive: Makes the whole game a NoDamageRun. Given her radar ability, it shouldn't be too hard, but screw up once, and you'll need to save scum.
*** Getting new companions: If you lose one, very far away from the town-hub, you'll have to navigate the gameworld without getting hit once, find the available companion of your choice, and continue.
* 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. Finding out that multiple people have been kidnapped, and finding out your a monster, must be horrible.]]