RahXephon is, simply put it as, Neon Genesis Evangelion but with the dysfunction, despair, and Kaballah and Judeo-Christian allusions replaced with transcendence and revelation, with musical imagery and Mayan lore added to the mix, and inspiration from Raideen and science fiction literature such as The Dandelion Girl, to produce a result that is thematically the total opposite to the bleakness of Evangelion's climax. Despite those, the series is not without its terrifying moments.
- The Dolems in general. They all have a very unsettling appearance. The horrible sounds they make combined with their body horror makes things worse.
- The Mu Phase of anyone of Mulian heritage, which causes their blood to turn blue and results in memory loss.
- Made worse by the fact that almost everyone in the cast is a Mulian due to that they're related to each other by blood or adoption, meaning that many of them ended up undergoing the Mu Phase.
- Tokyo Jupiter, the barrier surrounding the town, and how it's formed. It has the ability to to slow down time inside of it to one-fifth compared to the outside time.
- Ayato killing a dolem, only to find out that Asahina was linked to it and how she dies and its results.
- How about Ayato killing his first dolem? He's just seen Mishima (supposedly) get killed in front of his face. What does he do? He completely let's loose on the dolem, angrily strangling it until it shatters. It is no doubt awesome, but it's also terrifying, especially from the dolem's perspective.
- Let's talk about Mishima for a minute: she's actually a cosmic force named Ixtli. Think of a more benevolent version of Pennywise the Dancing Clown but with, ironically, creepier powers. It can manipulate people's memories and bend them to it's every whim. That may not sound so bad, but imagine what would happen if you were caught in it's sights.