So toward the end it is mentioned that people used various parts of Junko's body for various reasons, like one person transplanting Junko's eye into their head or Komaeda attaching her hand to his own arm. But that shouldn't be possible at all. If her body was flattened during the Detention part of the execution, how was any part of her that salvageable?
It's possible they were too caught up in their obsession to CARE whether the parts were actually salvagable or not. Komaeda mentions he can't actually MOVE his left hand...
I would think that the reason he couldn't move it was because the surgery to attach it wasn't done properly. Most likely, he actually cut off his own hand and just stitched hers onto the stump. Going by how crazy the Despair students are said to be, it wouldn't be surprising if they took her body parts and mutilated themselves to attach them without any medical help, because that just gives them more despair and shows how far off the rocker they are. And even if that's not the case, it still doesn't explain how there were parts of Junko still around when her body should have been pulverized to a pulp- literally. The Detention execution didn't dismember her, it squashed her! And going by how big the block was and how she was positioned, there should be nothing left of her that isn't flattened, let alone perfectly intact like her hand or eye. Of course, this is Dangan Ronpa so there probably is no reasonable explanation for how or why.
It's probably Mukuro's.
Even in that case, while her hand was salvageable, her eye probably was not. Of course, that might make it even MORE despair inducing.
Gundam's execution isn't an ironic death at all — it's exactly the kind of romantic death they claim they want just before going to the execution. Why did Monobear choose to do that instead of twisting the knife at the last moment like he usually does?
It's ironic because he's trampled by animals. On top of that, the magical circle he draws to protect himself does a grand total of jack shit — much like how all his posturing and grand declarations amounted to nothing. And the being lifted off to heaven by angel animals, assuming Monobear's responsible for staging that part, mocks the Dark Overlord image he's built around himself.
Monobear didn't seem to have control over the magic circle. That's ironic from a literary perspective, but not from an in-universe one. And while being carried off to Heaven may have subverted the dark overlord thing, the "lifted up to the skies to be immortalized in the stars" is the kind of thing he seemed to want in his pre-execution spiel. The whole thing is just very romantic and fantastical in tone, but seems absent of mockery like, say, Celes' was. Maybe the irony is supposed to be subtler than normal and I'm just not seeing it, I don't know.
No, he didn't. Gundam did. That's part of the irony — Gundam's using the powers he bragged so much about to try and protect himself... and they fail. Not because Monobear interfered with them at all — they just flat didn't work.
This execution is clearly ironic in-universe since Monokuma is using animals to kill the ultimate animal breeder. Nothing subtle about the irony of turning one's talent against them by having them murdered by the most obvious aspect of said talent. If that isn't "ironic" enough then the execution is also about how Gundam's true talent (or true self if you prefer) renders all aspects of his "Evil overlord" routine pointless since being killed by animals (mostly accidents) is a very common cause of death for people who work with them a lot (i.e. an otherwise ordinary death for an individual who puts so much effort in being special), just like the point of Celes' execution.
In the second trial, why does Peko do that spiel about how the students should let her go free because she's Kirakira and needs to do justice etc. if she wanted to get pinned as the culprit? If the students did as she asked, they most likely would have voted for Kuzuryuu instead (since he was the most suspicious next to her), which would have utterly ruined her plan.
That's all about staying in-character and convincing them she's really Kirakira. She doesn't really expect them to listen to her; she's just playing her role to the hilt. Making it look good.
In chapter 2, why did Peko choose such an absurd story for her alibi? People in the Let's Play thread were speculating that it couldn't possibly be her, because who in the world would make their alibi for murder "I went looking for the other islands and they just weren't there"? It's too unbelievable — it would place her under suspicion immediately. Why didn't she just say she went for a swim instead of also making up a story about nonexistent islands?
Because she wants to be caught. Getting the others to suspect and finger her for the murder is all part of her larger gambit to save Kuzuryuu. But offering no alibi whatsoever would look too suspicious, so instead she gives one that the others might accept on its face... until Fridge Logic kicks in and they look at it a little harder.
In the final trial, when Makoto, Kyouko and Byakuya enter the virtual reality, shouldn't their memories of being in the virtual reality have been erased when the forced shutdown commenced? They say so themselves that in the event of a forced shutdown, any memories they obtain within the virtual reality will be erased when they are brought back to the real world.
Perhaps this is proof that this wasn't true after all - for them or for the others.
A crapload of things in chapter 3.
Tsumiki had to have taken the camera from the hospital to the club. If that's the case, then how did Kuzuryuu not notice that she had it on her?
If you look closely at the scene when Hinata first discovers Mioda's dead body, you'll notice that the wiped bloodstain isn't there. But we later learn that it should be; it had been there since Saionji had died, which was long before Hinata first found Mioda.
Were they going to explain the reason why Mioda's slippers had blood on them, yet didn't leave bloody footprints? Because they bring up the point that it's strange that she didn't leave any footprints despite there being blood on her slippers, yet they never give an explanation how that could be!
If Saionji went to the club because she couldn't put on her clothes properly, then why was she fully dressed when on the pillar? Yeah, her clothes were in disarray, but they were on! Her obi was clearly tied, just not in the right place. Did Tsumiki take care to, not only clothe her, but do it improperly?
How was Sonia able to get into Saionji's room before Hinata, when Hinata had the only key? The door was locked; did Saionji forget to lock her door, but was careful to hide the key deep in her clothes, and then Sonia go into her room later and lock the door while she was inside?
How did Tsumiki cut off the video feed? She was on the ladder, reaching for the noose when Hinata suddenly couldn't see anything anymore. It's heavily implied that the candle did go out, and that the camera was destroyed once she got to the club, but either way, how was she able to ensure that Hinata's screen would go dark the instant she wanted it to?
Why would Tsumiki strangle Mioda instead of just hanging her? It's implied (or, at least, the only explanation is) that, after strangling her, Tsumiki put the noose around Mioda's neck, lowered the lighting rig, attached the other end of the rope to the rig, and then raised the rig back up again. But she could have easily just skipped the strangling part and hung her; then, the most decisive piece of evidence against her, the rope, wouldn't have proven anything, and she wouldn't have had to lie about Mioda's cause of death!
Tsumiki's original plan was to emulate the movie by having her victim be hanged. But, why? There's no reason why she would do a copycat murder if her original plan only called for one victim. Fortunately for her, a second one came along, and she was able to confuse the order of events, but why emulate the movie if it's just going to end up clearing the most immediately suspicious person (Hinata) as a suspect? Yeah, she might have assumed that everyone had seen the film, but all the same, there was no purpose to doing a copycat murder if it wouldn't have caused confusion in the case of there only being one victim, as she had planned!
Why was Nidai excused from participating in the Class Trial? That was a blatant violation of the rules, regardless of his condition. The rules, which Monokuma holds as sacred, stated that attendance was mandatory, and it doesn't mention that those who aren't physically up to it are excused (unless you're dead, of course). Heck, they were able to meet the fully-functional mecha-Nidai immediately after the trial was over, so it's hard to see how he could have been fine after the trial, but not before. And even if he only did become functional during the trial, why didn't Monokuma just wait an extra hour before starting the trial? Now, obviously, it wouldn't have been near as dramatic to have had Nidai show up right before the trial, since we would have had to just ignore the fact that he's a robot while figuring out the murder, but all the same, it doesn't make any sense why Monokuma would excuse him from participating.
Komaeda, unlike normal, was 100% against the culprit this time. The reason he gives is that these murders were done purely to create despair and not in the hope of getting out. But how did he know that? He wouldn't have any way of knowing what was going on through the culprit's head; there's no reason to assume that the culprit would have done anything different had they been acting out of hope rather than despair.
If Hinata ran as fast as he could from the hospital to the club, then almost immediately left the club and ran to the motel, how did Tsumiki have time to do everything she did? Not only that, but the Climax Logic segment implies that she was hiding out behind the club when Hinata left for the motel. Even if she left immediately after Hinata, she still would have needed to get behind the building without him noticing, and he was only inside for... 15 seconds before heading for the motel? And, once again, that assumes that she sprinted to the club immediately after Hinata did; before she could've left, she needed to hide everything she used to fake the feed (ladder, rope, candle, hospital gown), meet up with and explain the situation to Kuzuryuu, then get to the club. The only conclusion I can come up with is that the Climax Logic segment was wrong and Tsumiki was still running to the club when Hinata left, but even then, it's hard to see how she had time. And that's not even going into how long it would have taken Kuzuryuu to get to the hospital from the first island, considering that he left after the morning announcement, when Hinata was already sprinting to the club, and he was walking. The timing of this incident makes no sense whatsoever!