If you are actually on the doctor's romance route, you accidentally condemn Yuuya to this fate, and in gratitude the doctor sends you a lovely Christmas dinner months later. Then, on Valentine's Day, he allows you to find the remains of yet another student, only to reveal that You Have Outlived Your Usefulness... your usefulness living, that is. He then describes in loving detail how he plans to dissect you, preserve your head as a gesture of affection, and examine your insides most... intimately.
The "Bad Boys Love" route in the paid game starts with the heroine's death, then lovingly sandwiches layers of this trope with breaking every cutie in the game, and the player as well. Mostly courtesy of Shuu. Highlights include Ryouta crossing the Despair Event Horizon and consenting to being modified by Shuu into a bioweapon for use against the rest of humanity when they attempt to slaughter everybirdy left in the school, a graphic (described) flashback to the heroine's death by suffocation via The Virus that Ryouta is now a host for, an even more heartbreaking flashback to the previous host of said virus, Nageki, being Driven to Suicide and setting himself on fire so that nothing will remain of himself to spread the virus (which fails), Kazuaki aka Hitori flipping out and trying to vivisect Ryouta, untrained, to remove Nageki's transplanted organs and bring what's left of Nageki back with him, and the horrifying, bloody, sickle-clawed robot Labor-9 lurching after Ryouta and the other birds until they short-circuit it with a taser, only to be informed that Labor-9 was actually a cyborg with the heroine's missing brain and they just murdered the heroine again.
The manga and supplementary material talk about how in 2070 the Sumatra Flu swept the world and reduced the human population to 30%. The remaining humans then tried to exterminate the birds which were spreading the disease to them, but this backfired and humans and birds warred for thirty years. At the end of it the human population had been reduced to 4.6% of what it was in 2070, and humans were forced to live in the wilderness and not allowed to self-govern. Seventy years later there are still skirmishes between birds and humans, savage enough that the Hawk Party wants to just eliminate them all.
Anghel perceives an alternate, fantastical reality where everybirdie is more human-shaped and it's like a fantasy RPG, complete with more dramatic names for everything. Okay. The thing is, though, that this reality still reflects the "real" one, and in some disturbing ways. Narcolepsy-sensei assisted another bird to suicide, though the bird didn't really want to die, and stole his identity. So what does Anghel see when he looks at him? This◊.
The reason behind his alternate perceptions is scary too. Poor bird secretes hallucinogenic pheromones, but he lacks immunity towards them. There is a hint that those pheromones also act as some sort of airborne neurotransmitter, meaning that he not only is biologically trapped into his hallucinated world, but also he can bring people into it.. and can get info from them to fill the gaps in his worldbuilding.
Holiday Star has some.
The King is a comical figure in the third story... but there are flashes, when he gets especially upset, when he seems to be sprouting a second head. In the fourth story the comedy is lost, as he becomes truly nightmarish. His "Increased" form shown in the image above is a bloody quail corpse with many long, branching, serpentine heads flowing up out of it. If the heroine gets too reckless fighting him, her kick gets her foot stuck in his chest and she is absorbed into his twisted hivemind. There's also his backstory.
The moment when The King talks to Yuuya about how all he does is break eggs is horrifying enough before they add the sound of crunching eggs in the background.
For the most part, the manga is pure silliness with little moments of creepy here and there, like the aforementioned backstory to the setting. Then you get to Chapter 12, which is about Nageki and Hitori in the orphanage. ...The same orphanage that was mentioned in BBL, the one which was visited by human extremists who slaughtered everyone but those two, and this led to the discovery that Nageki was harboring a virus lethal to humans. This chapter is all sweet silliness except for Nageki's illness making him steadily weaker, but in the background behind the panels there are splatters, getting darker and more extensive the farther you get, until the last page, which is partially obscured by blood.