Considering the source material, it shouldn't come as a surprise that there's lot of Nightmare Fuel to be encountered.
Nightmare Fuel in Going another Way:
- The Angels of course are Nightmare Fuel in themselves, with being monsters out of nowhere for normal people. However, some of them do stick out.
- Sahaquiel is said to have enough destructive power that his suicide run would destroy half of Honshu. Just think about it...
- Iruel acts like an infection. It can infect any kind of techology. Wonderful Paranoia Fuel...
- Witnessing Liliel's digestion is nasty when considering what exactly she eats.
- Arael is totally Ax-Crazy and it's really disturbing to real the thoughts of a complete psychopath.
- Armisael's calm serene demanor is downright creepy. Even when he talks about absorbing Shinji and Rei into himself, it doesn't change.
- Shinji watched his mother dissolved at age three not because of any kind of plan, but because of pure coincidence, because his sitter got sick that day. A simple coincidence traumatized a child.
- Shinji describing the phantom injuries he suffered in battle against Shamshel. To him it felt very real.
- The area in which Rei's apartment is situated is described in more detail. Just reading the nighborhood Rei lives in makes you wonder why nothing bad ever happened to Rei - though perhaps security did exist for her.
- Additionally, the description of Rei's apartment is vomit-inducing. What animation managed to hide is described in loving detail.
- Shinji's visions of the post Third Impact world are disturbing because they do nothing but describe what's seen at the end of End of Evangelion.
- Rei does have a dream about being naked in class. Nothing unusual up to that point. Then she suddenly stands naked in front of Gendo, who says she will be replaced. Now it's not so funny anymore, isn't it? To make it worse, that was Rei's very first dream.
- The aftermath of Gaghiel's attack was only glossed over in canon. Here we are confronted with how much death and injury it caused.
- What was done to Mayumi. Poor girl is in constant pain without special drugs and she has no idea what exactly had been put into her. Once it becomes clear that SEELE used her as incubator to test the growth of an artificial S²-engine and the damn thing is removed from her, it's shocking she'd had that thing inside her the entire time.
- Worse, this implies that for the S² of the mass-produced Evangelions, SEELE used more victims.
- Leliel's destruction. It's so horrible that Maya has to vomit.
- The suicide of Kyoko Zeppelin Soryu (or at least her body) is described from Asuka's perspective - an Asuka who had been five years old when it happened. Her perspective makes it worse than it already is.
- The batlle of Tokyo-3 has serval "highlights", but the worst are without doubt the flamethrower troops advancing through the railway tunnel to storm the geofront. It's described in sickening detail how they burn the defenders to death with their flames and show no mercy.