The setting about the Apocalypse Virus in general of how it crystallizes many innocent people such as the outbreak of Lost Christmas.
GHQ is no exception as they rule Japan with an iron fist and is willing to kill civilians as possible.
The first two times Shu pulls out Souta's Void on-screen. While most people seem just slightly in pain (or sometimes pleasure) when having theirs removed, the first time Souta bends back unnaturally and his eyes roll up in his head, and the second time he sounds like he's screaming in agony, not to mention Shu runs at him and plunges his hand directly through Souta's chest, and the viewer gets to see Souta, easily one of the shortest and slightest members of the cast, get lifted off his feet and hang in the air off Shu's hand.
The Leukocyte satellite's power that can devastate the lands, and that's only 3% of its power.
Segai's crazed face before he activates the genomic resonance in Episode 10.
Mana Ouma herself, as she is the first person infected by the Apocalypse Virus to become insane in the process.
The way Mana stalks Shu in his childhood and tell him that she wants to marry him is unsettling.
How about at the church, Mana ordered an unnerved kid!Gai in shooting a Christmas star with a gun that reflects back to injure Gai in return? Then, Shu rejected Mana and caused Lost Christmas in the first place.
Mana's subconscious takes over Inori's body in doing things like killing a few students, injuring Arisa's hand with a sharp crystal, and nearly rapes Shu.
Once Mana is fully revived in the final episode, her infected persona becomes more dangerous, as she spreads the virus worldwide.
Hare's death. Yikes.
Seeing Shu becoming a tyrant after Hare's death and ruling his kingdom by ranking each void is unnerving.
What's worse later on is the student body turn against Shu after figuring out that they will die if their Voids are destroyed. Being Evil Sucks, indeed.