After learning the first murderer's motives, Togami tries to get Monobear to take him instead of executing them.
Hinata's struggles to reconcile the friend he thought he knew with the guy who was willing to randomly kill somebody.
Togami showing Hinata the note, and outlining all the ways he failed as a leader.
Hinata: Togami, I was there too. I didn't think to search it either— Togami: But you weren't responsible for everyone!
Togami's obvious hurt at Koizumi's ongoing distrust of him.
After all the hard work Togami and the others put into keeping anyone from accessing Monobear's second motive, the exact moment when they fail — and the circumstances — is quite painful. Hinata had no idea that Pekoyama and Kuzuryuu were the worst possible combination of guards he could come up with...
Pekoyama and Kuzuryuu's private discussion after he plays Twilight Syndrome. Even harsher after one realizes what the last thing she ever says to him is.
The Hope Spot before the second murder, where Pekoyama is pulled from the wreckage of her cabin, badly burned but still alive. She doesn't even respond to Kuzuryuu before passing...
After the second murder, Togami reaffirms his promise to everyone that he will do everything in his power to protect them. However, most of the students wander off before he can finish.
Kuzuryuu's Despair Speech after realizing that Togami and Hinata suspect he might be involved in the second murder.
The Reveal of who committed the second murder, as they confess their crime, calmly laying out their reasoning. Sonia witnessed Kuzuryuu playing the game, and spied on them afterwards. After watching Pekoyama play Lady Macbeth to her young master, she decided to kill her, figuring that without her influence he wouldn't be capable of murder.
Everyone's reactions to this. Particularly Tanaka and Souda, both of whom vote for the former rather than participate in sending her to her death.
The second execution. Faced with death by being rent apart by a slavering wolf, Sonia remains calm... until she looks to the audience for a sign of the empathy they showed Hanamura and can't find any. She dies screaming.
Chapter 2 ends, as Chapter 1 did, with how many days are left in the mysterious countdown: 13. In Super Dangan Ronpa 2, how many days were left after the second trial? 15. For all of his careful planning, Togami only delayed the second motive claiming a victim by two days. Awesome in some ways, but you can tell he doesn't see it that way.
The morning after the second trial. Several survivors don't show up for breakfast, and there's a bunch of drama over the Shrine to the Fallen, leading to Saionji attacking Souda while he pleads for help. Togami also gives him a vicious dressing-down, pointing out how he didn't really know Sonia at all, and his blind insistence that she was framed only proves that he's the least qualified to set up any sort of memorial to her.
In the second part of Chapter 3, Togami resigns as leader. Making this sting even worse is how Koizumi coldly dismisses this: like Togami himself, she only focuses on his failures.
Then there's his reaction to Nanami revealing thatshe knows he's the SHSL Imposter. While he's had moments proving he's Not So Stoic before, here he absolutely freaks out, and nearly murders her in his panic.
It's worth noting that the second trial has been at least as hard on Koizumi as it has been on Togami, and it's quite sad when you think about all Koizumi's been through. She gets accused of covering up the murder of someone she doesn't even remember. When she argues that she considered the victim in the trial to be a friend, she gets to see footage of Pekoyama trying to convince Kuzuryuu to kill her. And then Sonia, acting on what she overheard, kills Pekoyama in part to give Koizumi a chance to live, something that Koizumi is not happy about, to say the least. Blaming Togami is her way of avoiding confronting her blaming herself for what happened, and although her decisions are different, her decisions are affected by her emotions as much as Togami's are.
In Part 3 of Chapter 3, Hinata silently notes the hypocrisy Koizumi shows during their meeting. The whole point of the gathering is to try and unite everyone after the second trial and Togami stepping down, yet she tells two of the most ostracized members to "Shut up and get out," and lets Saionji insult them. And nobody stands up to stop this. Great unity, guys.