This game is the subject of an ongoing LP and translation effortnote (as of this writing, the LP is currently at the start of Chapter 3). A temporary spoiler-free page for this game has been set up HERE. Readers of the LP who wish to avoid being spoiled should go there. While this page uses spoiler tags, it still covers the contents of the entire game. Those who are spoiler-adverse may wish to err on the side of caution.
Once again, each of the executions is tailored to the murderer. For instance, the first murderer, Hanamura, was blatantly perverted and hit on everyone, ignoring any protests. In other words, he acted like they were just there for his enjoyment — like pieces of meat. Their execution involves being battered and fried up like a piece of meat.
Also, before Hanamura is even proven to be the culprit, you discover that the reason he insists on being called a "Chef" instead of a "Cook" is because he's lying about how sophisticated he really is—as it turns out, he grew up in the country, not in the city as he claimed. So what cooking method does Monobear use in his execution? Monobear flash-fries him...a cooking method associated with the poorer classes!
The second murderer gets a doubly ironic punishment. Pekoyama cast herself as Kuzuryuu's puppet against his own wishes; Monobear thusly transforms her into a puppet and has her 'kill' others. As much as she cared for her young master, she unintentionally hurt him by embracing the role he wanted her to reject; Monobear ensures she hurts him physically as well.
The third, after breaking down after being revealed, Mikan collects herself and tries to Face Death with Dignity, willingly going to her execution. Monobear ensures it's extremely humiliating and degrading, mirroring the horrid treatment she couldn't escape at the hands of her peers.
Don't forget how she had all of her memories returned to her right before she was executed. Considering how she was one of the SHSL Despair, it's no wonder why she seemed to have enjoyed herself a little too much.
Also, a possibly more vulgar interpretation, but... As a member of SHSL Despair, the person Mikan loved was more than likely Junko. Her execution is easily the most suggestive in the game, with a split-second screen of Mikan (naked) apparently having an orgasm as she's shot into space on a giant, pulsing fist. Given that Junko-as-Monobear frequently makes lewd comments about her classmates, it's likely that this was intentional. Also, it fits her position as the game's unwilling fanservice girl.
In her opening bio, it says they dislike 'big things'. So what does Monobear do? Stick her with a big needle, which makes her bed turn into a big arm, and she's shot into space.
The fourth is given a Negated Moment of Awesome. Gundam always bragged about his arcane abilities and that his title was just a front. During his execution, he attempts to prove his claims were true... to no avail.
Why there was no avail is still up for speculation.
The fifth is maneuvered into a no-win situation, both by the actions of their accidental victim and by Monobear. He also deliberately manufactures a Hope Spot in order to mock their ideals.
In the very beginning of Chapter 1, when Monobear reveals that there is a traitor in the midst of the students, Togami is quite adamant that there is no traitor, and even asks everyone to abandon the idea that there is. Why? Because he believes Monobear is talking about him, the Super High School Level Impostor, and he doesn't want his cover blown.
In the original game, Mukuro has a hairclip of a rabbit when she disguises herself as Junko Enoshima. Given that Mukuro reveals to Naegi that she sometimes wishes she had tried different things - basically giving herself a little hope for her future, it is especially interesting that Usami, the teacher meant to teach the students the value of friendship and hope, is a rabbit. This is most likely intentional, given that they have the same color pattern and eyes.
Why does Nanami take a while to respond, sometimes? It might be that she's buffering or loading a response.
Komaeda's jacket design features red blocks and the bottom begins to cut off in hard edges. The red blocks look like pixel blocks and the bottom of his jacket is disintegrating in a block pixel fashion. Not only does this link with how the islands are a computer simulation, but they can be connected with Komaeda's decaying, disintegrating mind.
There is a piece of symbolism regarding Hinata's Exotic Eye Designs: compare them to Izuru Kamukura's eyes. Hinata's eyes are a prohibition symbol, Izuru's are a target radar. This showes two things:
Hinata was talentless, so he considered himself worthless; he negated his personality to became Izuru, whose sole drive and aim is gaining talents.
The computer simulation was built to give the SHSL Despair members new memories, negating the old ones. Hinata regains the red eyes when he decides to take his future in his own hands and follow his own objectives.
Related to Komaeda's Free Time Events: unless you had at least one scene with him before the first trial, you won't be able to get any more scenes with him. This is understandable, since Hinata won't want to be close with a psychopath... unless he knew the "friendlier" side of Komaeda first, and so have a reason to keep trying to reach for him.
There was a similar scenario in the first game, too: Genocider Syo's Free Time Scenes. Although what changes is that A) Naegi is much more optimistic and willing to make friends than Hinata, and B) Syo has already admitted that she can't and won't kill anyone.
Why didn't Komaeda realize that Nanami was the traitor sooner? Being a self-proclaimed SHSL fanboy, he has admitted to looking up information regarding his classmates before coming to the school. And indeed - he provides some extra information about each student in the prologue as they do their introductions. All except for two - Hinata and Nanami. The former because Hinata was never a proper Hope's Peak student, the latter because she doesn't even exist in the real world. In fact, Nanami herself seemed surprised when the file containing all their profiles included hers - suggesting that she wasn't actually based on an existing SHSL student and that her 'profile' was just a dummy made by Monokuma. Therefore, Komaeda wouldn't have been able to find any information on her - which should've been immediately suspicious when he's considering possible candidates for the traitor.
Regarding the "Despair Fever" in chapter 3:
Komaeda is a fervent follower of Hope, so he's hit the most by Despair. Also, he has Brutal Honesty unless he has good reason not to: now he can only lie.
Owari loses her strength and fervor, since she was hit hard by being indirectly responsible for Nidai's injuries.
Mioda gets the lesser effects, as she is made Comically Serious... but still comical.
And considering Mikan's past... yeah....
For the English release Super Dangan Ronpa 2, the subtitle was changed from "Goodbye Despair Academy" to "Goodbye Despair" however this subtitle fits just as well because the characters being killed off in this game are actually all members of Super High-School Level/Ultimate Despair and the original purpose of the virtual simulation they are trapped in was to reform them from Ultimate Despair via deprogramming.
Among the various Body Horror things that happen to Junko's body, we learn that someone "removed her eye and put it in their own socket, perhaps to see her despair." Which one of the kids has mismatched eyes? Which one is gray? WHICH ONE IS THE SCAR OVER?
This is actually jossed since Gundam's eyes are both naturally gray (the red eye is a contact) and the scar is most likely make up. Not to mention the silhouette of the person who removed their eye showed that it was the right eye, not the left which is what Gundam's scar would imply. However, there is a student who did lose his right eye over the course of the game...
Hiyoko bullies and insults everyone, but particularly seems to like picking on Mikan and Souda, since they give her the best reactions. Mikan's Free Times eventually reveal that she was bullied so severely growing up that she struggles with the concept of not having to be utterly degraded and abused to get attention, while Souda's reveal he was a Shrinking Violet who was bullied all through middle school, and is trying to change his image to escape that.
This gets even WORSE when one takes into account Chapter 2, which reveals Hiyoko was just as big a bully to Mikan at Hope's Peak, driving home how badly she had any hope of receiving better treatment from her peers there crushed.
Souda regards Hinata as his 'Soul Friend', something which is largely Played for Laughs. Then one reaches the endgame, factors in his Free Times, and realizes both of them were willing to give up who they used to be in order to reach their goals, with one of them MUCH more successful at leaving his old identity behind.
At the end of the first trial, before being executed, Hanamura is extremely worried about his frail old mother since he came to Hope's Peak Acadamy to help her. When he asks if his mother is ok, Monobear refuses to answer. Fast forward to the end of the game, when it's mentioned that some of the students, who happened to be SHSL Despair, sacrificed their family to Junko. Therefore, it's entirely possible that Hanamura joyfully killed his mom who he was so worried about
Apart from Nanami, every single member of the main cast had been broken down into destructive, despair-motivated monsters "without a shred of humanity left" by Enoshima. This is easy to dissociate because those memories have been taken away...but think about it on an individual basis. Every single member of the class. Even the sweetest, kindest ones. Even Nidai. Even Sonia. Even the Super High School Level Impostor. Your very favorite character killed their family and friends and hundreds more in awful ways and rejoiced in the despair it brought them. The player character is a mass murderer. Even with their memories gone it's hard to think of them sympathetically without totally dissociating this.
Related: That picture of an older Saionji was probably taken when she was in this state. Which begs the question: why is she smiling?
Also related to the above. If Komaeda is already crazy without his memories then how insane was he before his memories were taken away. We get a glimpse of his insanity but how much is his hope talk really a load of bull before his memories was taken away or if he really was hopeful person that avoided that route and is only crazy because Junko has a firm grip on him compared to the other characters.
Mikan telling Komaeda that she didn't kill out of Despair, she killed out of "Love". Why Fridge Horror? It's implied that [SPOILERS AHEAD]the person she "loved" and wanted to impress was Junko Fucking Enoshima.
It might have not just been her, in the game and during his free time events Souda makes it clear he has a preference for blondes (like Sonia) and that looking the way he does has a tendency to attract the attention of "those gaudy popular girls" who terrified him. Now who have we met before who fits these descriptions perfectly? Junko Enoshima, the SHSL despair fashionista. The horror aspects come from the fact that as stated above as the SHSL despair mechanic he was probably the one who made the machines used in her executions and this means he might have done it because he fell in love with Junko just like Mikan did and this was his way of expressing it to her.