The second trial of the first Danganronpa was the point at which I became really emotionally invested in this game, and, although I can see why it ignited so much controversy in the fandom, it remains one of my favourite cases in the whole series. Just thinking about it makes me sad.
When I first played the trial (or, well, technically when I first read it in a fan-translated Let's Play), I genuinely had tears in my eyes. I started getting choked up the moment I realised Mondo hadn't switched the rooms and broken Chihiro's handbook in an effort to cover his tracks; he was trying to keep his promise to Chihiro. It's absolutely devastating.
Mondo didn't even try to dispose of the murder weapon. He just moved it, with the rest of the crime scene. He didn't try to remove evidence of his crime; his focus was on removing evidence of Chihiro's secret. He didn't confess, of course, but he did almost nothing to conceal his involvement, which makes me wonder how much he really wanted to get away with this.
You can really feel how much Mondo hates himself at the end of the trial. I don't think he had any intention of harming Chihiro when he agreed to meet up for training. But he was terrified of having his secret revealed, so on some level he was probably looking for a reason to kill someone, more volatile than usual, more violent than usual, and not much could have been worse for him at that moment than seeing someone so physically frail displaying mental strength so far surpassing his. A burst of spontaneous, violent rage, and he did something terrible and irreversible.
The room switch and the handbook-destruction say to me that Mondo immediately regretted his actions, but what could he do? He couldn't bring Chihiro back. All he could do was try to keep the promise he'd made to the person he'd just killed.
And then there's the fact that poor Chihiro admired him so much and obviously had no way of knowing why Mondo was reacting so badly, which is heartbreaking to think about. To make things worse, if you complete Chihiro's Free Time events, you end up suggesting Mondo as a training partner, so you essentially destroyed both of them.
I was really worried, when it became clear that Mondo had been the killer, that he might have killed Chihiro out of prejudice. But he didn't. The content of Chihiro's secret didn't matter; what mattered was that Chihiro had a big, important secret and was brave enough to tell Mondo about it, which intensified Mondo's hatred of himself for being imprisoned by his own secrets, which caused him to project that hatred. He killed Chihiro because he was jealous and confused and frightened and self-loathing and painfully lacking in self-control.
I'm not trying to claim that Mondo's actions weren't wrong. It's bad that he killed Chihiro! Obviously it's bad! It's terrible! But Mondo fascinates me because he does this awful thing and wants to take it back straight away. I don't think you can call it an accident, exactly, but it's a mistake, and he's in agony over it. The idea of killing someone in a terrible, unthinking moment and instantly regretting it and trying to make it up to them in whatever tiny, inadequate ways are left to you is just so painful.
I can't accept Mondo's actions, but I can at least view him with sympathy. In the end, this is Mondo's tragedy as well as Chihiro's.
If this interpretation of the second murder case works for you, you might be interested in my fic a little too late on AO3, in which Makoto realises Mondo might have been the killer and confronts him before the trial.