Warning! All spoilers below are unmarked.
- Monomi's "execution". Sure, she comes back to life in the next chapter, but hearing Usami's cheerful, energizing theme gradually fade into Monokuma's standard execution theme as she gets filled with lead and seeing Monomi's bullet-ridden bow gradually float to the ground like a fallen leaf as a sorrowful piano rendition of Monomi's theme plays just drives home the fact that Monomi's cute school trip is over, and Monokuma's killing game has begun.
- The climax of the first trial, made worse because the culprit had one of the least selfish motivations of any killer in the series: not only did Teruteru attempt to stop Nagito and end up killing Byakuya by mistake, the reason he wanted to leave the island was to return to his ill mother. Especially upsetting because most had regarded the culprit as a one-note Joke Character until that moment, the revelation was enough to move several characters in-game to tears. To make it worse, Teruteru starts bawling when it becomes obvious that he can't refute Hajime's argument, likely out of sheer horror at what Monokuma will do to him.
I'm sorry... everyone...I didn't want to sacrifice anyone. I just... had to do something...And yet... I ended up killing Byakuya instead of Nagito...Oh. I see.
- There's also the part in the flashback when he tries to convince himself that his mother will be fine while he's away. He chuckles and says that he knows his mother "won't lose to some illness," but then repeats it more weakly, making it clear that he's not convinced at all.
- On a related note, Chiaki points out that it's most likely that the reason Byakuya died instead of Nagito was that, thanks to his night vision goggles, he saw Teruteru moving under the floor and moved to shield Nagito from the skewer...because he promised everyone that no one would die under his supervision.
- Fridge Horror with the endgame revelations make Teruteru's back-story impossibly worse: if the disease didn't kill his beloved mother, then Teruteru — as a member of Ultimate Despair — most likely murdered her himself.
- You can visit the dead students' cottages after trial 5, and see what seems to be their final thoughts as they died. No prizes for what was on Teruteru's mind.
Ibuki: PP@040Yahoooooo23 '*?@@please 'A;@listento:.o./onesonnnnnng:@;@
- Then there's Ibuki's, which sound like she's pleading to sing one more song—or, considering how protracted her death (strangulation) was compared to most of the other victims, like she's begging for her life.
- Mahiru's message is about her feeling guilty about her covering up the death of Fuyuhiko's sister, wanting to fix her mistakes and go back to good times with her friends,
- Mikan's last thoughts are nothing but pleads for forgiveness and incessant laughter.
- Chiaki, true to her gamer nature, has the Konami Code at the beginning of her final message (perhaps she thought that a cheat code would help her friends escape this "game"), while the end of the message is an apology and a plea for the others to win.
- What Kazuichi says when he and Hajime find Mahiru's dead body, which really drives the tone of the game home.
Kazuichi: Hey... Hajime... Before this... we were having a great time right...? We were excited about going to the beach... We... were having a lot of fun... But... why... WHY DID SOMETHING LIKE THIS HAPPEN!? Someone, tell me!
- The second execution: Peko Pekoyama. Just before it begins, Fuyuhiko breaks down into tears and begins screaming that he never wanted Peko to be his tool - he just wanted her by his side. Monokuma takes control of Peko's body and forces her to fight an army of robots while Fuyuhiko tries to get to her, and she ends up slashing his face. Horrified, she cradles his body...and then the robots overwhelm her. Later, the characters discuss how lucky it was for Fuyuhiko to have gotten away in one piece, and they realize that Peko protected him as much as she was able to before she died.
Fuyuhiko: Please, Peko! Don't go! (breaks down in tears) I need you! Don't leave me!
- Before the third execution, Nagito expresses honest anger with the murderer for killing purely out of Despair rather than to inspire Hope. Mikan responds he's got it wrong: she killed out of love. When Nagito's shocked by this, she talks about how someone accepted her for who she was, with all her flaws... and adds that she feels sorry for Nagito, who's never felt that kind of love. It gets worse when you realize that the person she's talking about is Junko, who more-or-less brainwashed Mikan into joining Ultimate Despair and who probably never gave a crap about her at all.
Mikan: ...Huh? Is that all you can say? Ah, so in the end... you're all just a bunch of bullies, huh? Justifying your actions with fancy words... M-Making excuses for why it's not really your fault... (starts crying) E-Everyone always treats me like that... Always... "It's all her fault! She's the one with the problem!" (hysterical portrait) I'M DONE WITH THAT! YOU HEAR ME!? I'M DOOOOOOOOOOOOONE!
- Even if it was a Wounded Gazelle Gambit, Mikan's attempts to fight back are painful to watch, considering how shy and helpful she'd been up to that point. The other students try to help her when it becomes obvious that Hajime and Nagito have ganged up on her, until Chiaki makes everyone else stand down. With no one left defending her, Mikan's uglier side rears its head, making it look like she's finally snapped from the abuse she's suffered.
Hajime: Mikan... it's already over... After I go over your crime from the beginning and show that you have no arguments left... Please, just admit it already! In the end, at least let me believe in you!
- There's also how many people have trouble accepting that someone like her was the killer. Hajime's noticeably pained just before delivering his Closing Argument.
- And the aftermath was pretty sad as well. Everyone learned the dark side of Mikan and thought that all along, she hated them all for never standing up for her, and she died hating them. This just gets worse when The Reveal way later kicks in.
- The fourth trial and execution: Gundam Tanaka and Nekomaru Nidai. When the entire group was left with nothing to do but starve to death, these two decided to try to kill each other just in order to have a murder committed, and therefore get food to all the rest of the group who needed it. By the end of the trial, every character seems to understand that for Gundam and Nekomaru, this was actually their sacrifice to save the rest of the group from a prolonged and painful death.
- Not to mention Gundam saves his hamsters by placing them out of the way before facing his own death.
- His hamsters cry for him. And then his dead pets carry him to heaven...
- Sonia's reaction to the whole thing is saddening as well. Gundam is arguably the student she is the closest to and when she finds out he is the murderer she is completely shocked. Even so, she cries and pleads with Monokuma to not execute Gundam because she understands that he did it all for their sake. Gundam's last words are also what motivate Sonia to continue surviving and to not give up on the investigation in Chapter 5.
- Akane is usually the toughest and most aloof of the students, and the only time she's shown crying was when she was infected with the Despair disease. So seeing her genuinely sobbing while cradling Mecha!Nekomaru's head was especially heartbreaking. It gets worse when you learn about her life growing up. Akane never bothered to make close friends, or even learn any names, because there was always a chance they were going to die the next day. But at this point she had become extremely close to Nekomaru. She allowed herself to become close to another person, only to lose them. And it was soon after she almost lost him the first time too.
- In Chapter 5, you can see Fuyuhiko stopping at the memorial. He finds a picture of himself with Peko, who's been dead since the end of the second trial, and realizes that this was the only one of them together as friends and classmates. Hajime wonders if Fuyuhiko has been crying, and decides to leave him alone.
- The fifth trial and execution: The kids determined that Nagito committed suicide, and we figured that was it—vote him as the culprit, no one else has to die. Except that he actually set up an awful plot which created an accidental culprit, so even though the entire plan was set up and carried out by Nagito, the actual cause of death is laid upon none other than sweet little Chiaki. This was all part of Nagito's plot to kill the rest of them so that only the traitor would live, but Chiaki wouldn't allow that—as soon as she figured out the truth, she decided to sacrifice herself to save her friends, and that was truly one of the most unfair and heartbreaking moments of the entire game.
- The execution itself punches the player in the gut. In the previous chapter, it was pointed out that every murder in this game has been similar to a murder in the first game. The fifth execution in DR1 had Makoto escape and survive until the next game. Naturally, when Chiaki spots an exit door in her execution chamber and makes a run for it with Monomi, the player expects the same scene to play out. Nope! Chiaki and Monomi get trapped in a giant game of Tetris and just sit there miserably until Monokuma drops blocks on them and kills them. It doesn't help that he stretches out the moments before finally killing Chiaki forever.
- Another particularly heartbreaking moment is everyone's attempt to deny the fact that Chiaki is the culprit, especially Sonia. There is an instance where you have to play the counterargument game against Sonia, and instead of playing the usual high speed and volume theme that goes with the game, what instead plays is a quieter song appropriately named "All All Apologies". . It shows how much pain Hajime is going through... He really doesn't want to see one of his greatest friends dead, but at the same time, if he wants everyone else to live, he has no choice.
- On a related note, Monomi's PTA and her dialogue leading up to it. She's such a Bad Liar, everything she says about Chiaki is the exact reverse of their true relationship. She has a friend and she loves Chiaki.
- What really hammers it in is Hajime not doing his usual dramatic voice clips when breaking arguments and selecting the culprit. He's either completely silent or has new ones that reflect just how much he doesn't want to go through with this.
- The game also takes a departure from all the other trials. When the time comes to vote for the culprit, the game makes you vote for Chiaki yourself.
- Chiaki just has to act so damned cheerful about everything, too. She keeps encouraging you and dropping obvious hints and apologizing for everything with a sad smile on her face. Given the way she describes being the traitor and having no choice about being able to reveal herself...it almost seems like a relief to her to be able to finally tell everyone who she really is. Given that this means going to her death, and generally just how friendly and caring she acts throughout the game, keeping a secret like this must have well and truly been tearing her apart inside. It hurts a lot more when she's smiling so sweetly with a quiet theme playing and you have to choose her as The Mole.
- The most unfair thing about the entire situation is that Chiaki didn't really kill him. Nagito had placed a lethal poison inside one of the fire grenades and intentionally inhaled once it broke open. The only thing that prevented it from being ruled a suicide is the fact that Chiaki was the one who threw the poisoned grenade without even knowing it. Under Monokuma's rules, that still counts. The girl who was so adamant about protecting her friends and didn't have a malicious bone in her body ultimately ends up being convicted purely because of a technicality.
- It's later revealed in Dangan Ronpa 3 Despair Arc that Chiaki was a real student, and everybody got along with her and considered her a friend. It'd explain also why everybody was super duper upset even further.
- Then Dangan Ronpa 3 went and made it even worse: As it turns out, this is the second time they've seen Chiaki be executed, with the first time being why they all became Ultimate Despairs in the first place.
- When you find out that Nagito didn't just have a moment of trollish insanity when his aim was to kill everyone but the mole: He learnt that everybody, including himself, were the remaining members of Ultimate Despair and that the mole was from a foundation trying to purify the world from despair. Out of the horror of this truth, he aimed to kill himself and the rest of the people who once bought despair into the world, leaving the one person (the mole) who didn't cause any despair alive. Nagito's mental condition made him take this news so badly, that he wanted everybody who caused such despair to be gone from the world.
- In Chapter Six:
- One of the reasons Hajime's so wary about the Forced Shutdown is because it'll get rid of everything in the game world - and since Chiaki was an AI who doesn't exist outside of the game, they'll forget her entirely.
- Also during the final trial, the main reason why Fuyuhiko is reluctant to invoke the forced shutdown isn't because he doesn't want to go back to being Super High School Level Despair (although he's also against that) - it's because he wants to see Peko again.
- The part of the trial where Junko throws Hajime into an Imagine Spot where the game has reset and everyone is alive and well. They are all happy and acting like regular high school students, with no signs of despair. But it's all a sick lie that can't come true without severe consequences in the real world, and Hajime has no choice but to refute this "utopia".
- Everything about Izuru Kamukura, once you get past the Nightmare Fuel. He started out as an average Reserve Course student who just wanted to gain a talent and escape his second-class status, and ended as a mass murderer, bitter and bored with existence. Chapter 0 (the short scene at the end of Chapter 5) shows just how empty and apathetic he's become, with no trace of the cynical but good-hearted Hajime left.
- There's also Hajime's breakdown upon being confronted with this revelation, particularly in the English version. Johnny Yong Bosch did a really good job.
- Both himself and the other students have to come to terms with the fact that, since Hajime's personality was created for the game world from what remained of Izuru's memories, initiating the forced shutdown essentially means killing him. The other students may have been brainwashed by despair, but it would still be possible for them to return to who they used to be. Hajime and Chiaki, however, would be gone forever... and they wouldn't even remember them. Fortunately the epilogue shows Hajime is okay after all.
- Pretty much every character's backstory. Most notably:
- Peko Pekoyama: abandoned as a baby and raised to think of herself as only a tool to serve Fuyuhiko.
- Mikan Tsumiki: bullied so mercilessly that she thinks degrading herself is the only way to gain attention. She was also apparently abused by her family, and half the reason why she got into nursing was because she had to take care of her own wounds, as no one else would help her with them. Finally, it's implied that she was in love with Junko, who's the one behind the killing and had almost certainly been manipulating Mikan by taking advantage of her desire for affection and forgiveness.
- Kazuichi Souda: He was bullied in school to the point that he tried to completely reinvent himself into a tough guy jerk, because that's what his bullies were like and he associates that behavior with strength. He had only one friend in school and that friend ended up abandoning him after Kazuichi helped them cheat on a test and took the fall for them when both got caught, which only made his bully-induced trust issues worse and helped lead to the after-mentioned self-makeover. He was also implied to be abused by his father.
- Akane Owari: grew up in poverty and has worked in jobs were she was sexually harassed, all to gain money for her several siblings. In chapter 4, she says that the cheap room in the funhouse is a palace compared to her home.
- Nagito Komaeda: his life has been a constant cycle of bad luck and good luck which has included losing his parents in a plane crash, then gaining a massive inheritance, then him being kidnapped, then winning the lottery. Lately, he's also been diagnosed as terminally ill. This cycle has exhausted him so much that in his Dangan Island ending, it's revealed that he wanted to die on the island.
- Nekomaru Nidai: born with a heart defect so severe that he was told he wouldn't live past 20. Constantly bedridden and making frequent trips to the hospital, he was never able to join PE or play sports, and was teased a lot. Part of the reason he became a sports manager was to emulate his friend Daisuke, who had the same condition as him, but died before he could see his team succeed.
- Hiyoko Saionji: bullied and treated miserably by her family, who did things like intentionally give her food poisoning and put needles in her shoes out of jealousy over her talent. This abuse is likely what lead to her becoming so cruel and vicious toward others. The only person in her entire family who ever treated her kindly was her father. She genuinely tears up just from mentioning him.
- Gundham Tanaka: never had any friends growing up. The only source of companionship he had in his life was his mother, who tragically died when he was young, and the animals he began caring for. Beneath that dark overlord persona he's created, he's incredibly lonely. There are also hints that he may have been born out of wedlock and was rejected by both sides of his family.
- The final free time events often have Hajime making promises with the characters once they get off the island. Taking Chiaki to see all kinds of new places, helping Mikan change, learning to take photos with Mahiru, training with Nekomaru, etc. And he doesn't get the chance to fulfill many of them.
Chiaki: (lovey portrait) So... can you keep teaching me, Hajime...?Hajime: Yeah, of course. But in order to do that... We need to hurry up and get off this island.Chiaki: ... (sad smile) Don't ever forget about me. Even after you get out of here...Hajime: ...Huh?
- With the end Dangan Ronpa 3, he has a chance to fulfill all of them... except Chiaki's, which he never could. And she knows it too; from the moment Hajime makes the promise, all she can do is ask him to not forget her once he leaves her behind in the simulation. And he isn't allowed to know why until The Reveal.