Chase can attempt to rekindle his relationship with his ex-boyfriend Leo, who is shown to be very controlling and borderline abusive. However, this choice does trigger a bad ending.
While it’s negligible if it’s an actual death, one of the main protagonists Flynn is brutally burned at the end of his route, which would have resulted in his death if not for supernatural intervention.
Directly stated in Leo's route, Brian says he experienced genital torture as a child (which he pins on aliens, but that was likely a trauma response and was really done by his parents). Later in that route Chase viciously attacks Brian's genitals to escape.
In Jenna's route Brian intends to sew Chase's genitals to his legs, although he is never able to do it.
While it doesn't directly happen, Brian surrounds a noose with razors so that trying to keep yourself from suffocating will result in severing fingers.
Jenna's route contains a scene where several characters are graphically tortured. Jenna's route also contains a CG with a character's mutilated corpse.
There is a chance for several major characters to die throughout each route (mostly during the bad endings), however most prominently, Flynn is drowned at the end of TJ’s route.
Carl and Flynn have an unclear relationship status before the events of Echo (see Echo: Benefits), if you interpret them as having had a relationship each of them cheat in their own routes.
In a flashback in Jenna's route, Leo is manipulated into believing Chase was cheating on him, although it didn't really happen.
In Flynn's route it's directly stated that some of the men in the Smoke Room orgy are married.
Yes, not to a trans person, but in Jenna's route she gets birth/deadnamed quite a lot, and it's a big part of her relationship to other characters (namely Heather and Jeremy).
There are many suggestive scenes throughout the novel. Most notably, during Flynn’s route, he and Chase have sex, however there are no accompanying visuals.
ending depends on the route. carl, leo, and jenna have good and bad endings depending on player choice. flynn and tj only have one ending, but both are sad