Nightmare Fuel moments in Thousand Shinji:
- Shinji got stuck between his Khornate berserker Tsundere girlfriend and his Nurglite Yandere sister. That is a Love Triangle you would not wish on your worst enemy.
- Rei's apartment: imagine a place completely littered with trash, garbage and dead animals, where dozens of different kinds of moss and mold carpet the walls and where trespassers are killed by sick vermin who infects them with who-knows-what illness.
- Whenever one of Rei's clones dies, the replacement goes and collects the head and mounts it on an alter. She has a collection of her own heads. Chapter 13 has them talking to Rei.
- Rei's transformation in Reigle. The nicest, mildest way to describe her aspect is she "looked like a corpse that had been left in a hot swamp for a month."
- The fates of Gendo and SEELE. Their souls got stuck partially inside a wall in the properly-named Hall of Torments, permanently subject to endless, terrible pains, at the mercy of four very angry dark gods yearning for paying their pain back.
- The final chapter has the various gods explain the fan fic's events were all part of a big scheme because, the C'tan had all but won in the future. The C'tan and the Necrons established a base where Warp has next to no presence, and have wiped out any attack by the other factions of the galaxy. From there they started to expand the area warded off from the Warp and new Necron armies rose up across the galaxy, launching raids on the living so C'tan could feast on their souls in an unstoppable harvest that would leave all life as little more than cattle for the C'tan to feed on. The only chance at defeating them was completely re-write history so that the new Chaos Gods created by the fan fic could catch them completely unaware because time was rewritten causing the C'tan have long ruled the galaxy, with only organic Necrontyr as their followers, and have grown complacent in their victory.