[SPOILERS]
The protagonist is well aware that he is dying during the last few days of the game but opts not to say anything to anyone about it, except for Aigis and even then, it’s only because she already figured out what was happening.
There are stray dogs and cats throughout Tatsumi Port Island. Koromaru the dog is alone after his owner died, but is taken in by SEES and becomes a party member.
A little girl says her father hit her when she asked why her parents were getting a divorce. The Mom responded by saying it was the girl’s fault for asking them about the divorce so much.
The Tower social link character is an elderly monk who abuses alcohol to cope with his divorce. Junpei’s father is an alcoholic which has strained their relationship to the point that Junepei tries to stay away from home as much as possible.
Koromaru is a party member that fights shadows. At one point during Koromaru’s social link, he will growl at another dog. There is no dog fighting, though.
A cat dies off screen.
Details:
During Aigis’ social link, an old lady will ask you to help find her cat. After finding the cat, it will run away again later. The old lady will say the cat was unwell ran off to die alone. In a later social link stage, Aigis will go into a philosophical discussion on death and will once again mention the cat dying.
Some may find this storyline very upsetting even though there is no death shown on screen.
Additionally, cats may get lost in Tartarus and need rescuing. While it’s not explicitly stated, one can infer if they aren’t rescued then they won’t survive. Some of the cats when found are said to be in distress.
The previous comment is false. Kenji never actually enters a relationship with his teacher. Although Kenjj does have feelings for a teacher this isn’t reciprocated; Kenji misreads a tutoring session as a date, spreads rumours that he’s dating the teacher and almost gets her fired as a result until she explains to the school what’s really happening.
With that said there is a real instance of pedophillia in the game: another female teacher expresses romantic feelings for the underage main character in an anonymous online chat, not knowing it’s him she was taking to (the chat is anonymous but it’s very easily traced back to her based on rants she makes about her job). This never progresses to an actual relationship, but it’s still quite disgusting that she even expresses this interest to begin with.
A female main character is bullied by other girls. There isn’t much violence behind it, but they do trap her in the gym and lock her in for most of the day and half the night, only going back to let her go when by their own words “we were worried we would get in trouble if she commited suicide.”
There’s a scene where all the main characters are crucified on crosses to be killed as human sacrifices, but they are freed before their captor kills them.
There is a point where a Shadow causes the Protagonist and Yukari to black out, then once the protagonist recovers, it tries to manipulate him through a voice in his head to have sex with Yukari while she is still blacked out, however the protagonist refuses to do so and they both recover fine with no sexual assault taking place.
(Note: There is a dialogue option that has you respond “yes” to the shadows temptation but if you select this, the protagonist will say something’s wrong with his head, refuse anyway, and the dialogue sequence will keep looping until you continually refuse it)
During a boss fight against one of the human antagonists near the end of the game, when they are running out of health, they will overdose on a stimulant in a desperate attempt to regain their strength
Most of the party members have dead family members.
Certain Social Links mention dead family members (Hierophant, Moon, Star, likely more I’m forgetting), with one involving a family member dying during the events of the Social Link (Temperance).
These are all offscreen, and most happened before the games events.
The game's romance system allows for cheating, but this is entirely the player's choice and the game gives clear warnings beforehand. One Social Link also includes allusions to a past instance of cheating.
Protagonist awakens in a hospital after falling into a coma. An antagonist is confined in a hospital bed after their capture because of their repeated attempts of self-harm.
Main plot revolves around a “secret 25th hour” of the day most people aren’t consciously aware of, where monsters roam the world, attack people while they are sleeping, and leave them as soulless husks.
A character that’s 10 years old says he considered committing suicide several times after the death of his mother. He later plans to commit a murder-suicide when confronting her killer and comes close to going though with it but is interrupted.
The Sun social link character is dying of an unspecified terminal illness. His mother approaches you at the end of the game and tells you he has died from it.
Protagonists parents were killed in a car crash. A flashback shows the protagonist (who is roughly 6-7 years old at the time) emerging from the burning vehicle.