- Catharsis Factor: Andy Moczo detests Shinji Matou (a sentiment many fans of FSN share), so any time he appears his efforts to do anything productive will end in him being a Butt Monkey - but because he does go too far each and every time, his subsequent clobbering is complete Laser-Guided Karma and he avoids being an Ineffectual Sympathetic Villain.
- Complete Monster: Zouken Matou, as per canon. Here, though, we witness his assimilation of another person's essence without the slightest trace of remorse. To top that off, Saber and Shirou are both highly unsettled by him, while Kirei has an internal monologue reflecting how much the ancient parasite disgusts him. Even True Assassin - while not actually put off by him - notes the hypocrisy and selfish refusal to admit fault in Zouken when the old bastard complains about his situation.
- Crosses the Line Twice/Dude, Not Funny!: Chapter 25, specifically the scene where Shirou, being Mistaken for Pedophile (with Ilya largely and unashamedly responsible for it), is Played for Laughs; this is either hilariously over-the-top and fitting of the Breather Episode, or extremely distasteful Humour Dissonance which callously pokes fun at a serious problem in reality (and Shirou being trolled by Ilya is taken way too far, even for her).
- Les Yay: Caster Alter and Sakura's... mana transfer ritual.
- Nightmare Fuel: Chapter 15 contains a scene where we see Matou Zouken assimilate an innocent's essence as he performs a Grand Theft Me upon her body. Reading it is both horrifically creepy and heartbreaking.
- The Scrappy: Caster Alter, to readers who believe she has overstayed her welcome and survived situations she should not have too many times. Most such readers felt the character should have been an Arc Villain (and assumed as much) instead of lasting until the story's climax - which veers dangerously close to Villain Sue territory, if not necessarily crossing right into it.
- Shipper on Deck: Irisviel really, really wants Shirou to take care of Ilya. Make of this what you will.
- Tear Jerker: In Chapter 14, Shirou is visited by the disembodied spirit of Irisviel, who softly asks him to do his best to save Ilya.
- Berserker's death in Chapter 22, particularly his regret that he can't protect Ilya any longer, and as he passes she - despite being unconscious - seems to feel it, and starts to cry in her sleep.
- Rin going through the Matou household in Chapter 29. Especially the part where she finds evidence of what Shinji did to Sakura.
- Took a Level in Badass: Gilgamesh becomes even more badass than usual when he is pushed to the breaking point of his outrage and decides to deal judgment to the rest of the participants.
- The Woobie: Both Ilya and Sakura. The former seems to be becoming an Iron Woobie here, as well.
YMMV / Chaos Theory
Fate/Stay Night Fanfic