In general, any time someone learns about the original future and the horrible things they had done.
As Hajime starts writing down what happened in the original timeline, he hesitates the moment he has to write down when Chiaki's death happened. It goes to show just how much her death really affected him.
This exchange between an anon and Hajime after he first realizes he traveled back in time:
Anon: Hajime, you know what it means, right? you can save them. you can save Natsumi and Sato and Chiaki and all of the other reserve course kids. Hajime looks stunned and then he says: No, no, no, this can’t be real! This can’t!
Hibiki's reaction to hearing that the school is no longer allowing her to stay there and her parents have disowned her, making her homeless. You can tell that this is not what she wanted to hear after what happened with her sister.
Right after Hibiki confesses to Hajime, she has a hallucination of Kanade taunting her with the accusation that Hibiki is responsible for all the murders Kanade committed. The evil twin boasts that while she may be in jail, she's not letting that stop her, and that she's going to get revenge on Hibiki and all her friends. Hibiki ends up so affected by it that she tries to silt her throat. Thankfully Hajime talks her out of it and helps her recover.
After successfully taking down Kanade before she can take revenge on Class 77-B, Hajime breaks down in tears in front of Yoruko after having to die once again to stop the yandere along with thinking about Yasuke's multiverse theory and how he's potentially "abandoning" his friends by jumping into another timeline. Watching so many of the characters we'd grown to love get brutally murdered during Kanade's killing spree definitely took an emotional toll on both the survivors and the audience. Thank God for the Reset Button.
Kana backstabbing Chiaki and luring her and Hajime right into a trap. Chiaki was the only one who 100% believed Kana was telling the truth about everything and that she couldn't be wrong.
Kana's backstory. Her and Chiaki are actually long-lost half sisters after the latter's father seemingly cheated. While not the full story, she grew up believing their father just abandoned her and her mother and while they lived a comfortable life, Kana could see how much her mother was struggling. Even then, Kana finds that she can't hate Chiaki, just because the latter is just so nice. The true story about why Kana and Chiaki are half siblings and why they never met. In truth, Chiaki's parents were very close friends with Kana's mother. When Misako's boyfriend proposed, she wanted a child, but he was sterile. Due to how close they all were, Tenmei offered to be the sperm donor, with the group having the intention of raising the girls together. However, Misako's boyfriend forced Misako to cut contact with the Nanamis, then bailed on her less then a year after Kana was born. Once Misako told Kana about that, she repeated it to Maverick, who twisted it to convince Kana that she was robbed of a father because of Chiaki in order to pit the two girls against each other. Both Chiaki and Kana are rather upset to learn that they could have been sisters this whole time.
When Fuyuhiko tries to convince his father to let him help Hajime and the others on the island, not only is he dismissive of him, he also refers to Peko as a toolright to her face. Later on, when an anon tries to apologize to her about it, Peko says it's fine because she is a tool. Fuyuhiko's pained sprite just adds to it.
When talking with Yoruko about their plans for the future once all this is over, Sora admits that she can't really imagine it being over. Sora's never known what a normal life is like; her entire life has been violence or the calm before violence, and she's terrified that maybe this is the setup for some new plan and their future kids will suffer for it.
All of the scenes of Kana in the hospital. She's trying to keep up a happy face and reassure everyone that she'll be fine, but she admits to Chiaki in private that she knows she most likely won't make it. Chiaki leaves the room following that conversation sobbing, especially because Kana had talked about all the things she wanted to do with her life.
Kana's death, full stop. This is the first time that the group failed to prevent someone from losing their life simply because there was nothing they could do.
Akemi briefly thinks that Rumi, the girl who she's fallen in love with, only hung out with her to protect her, when Rumi genuinely truly cares about what happens because she loves her and not just for the sake of the mission. Despite this, Akemi is heartbroken at the possibility and has to leave to rethink their relationship. Also doubles as Nightmare Fuel as being alone was what led to her death in the previous timeline.
Mizuta. Just...everything about Takehara Mizuta After losing all his money during Japan's Lost Era, he fell in with Junko who essentially blackmailed him into funding all of her projects and using him to get the Despair she craves. Then, after finally finding happiness with a woman he loves very much, she dies giving birth to their daughter Marin, causing him to live in constant fear that Junko might do something to her. After being found out by the Quantum Crew, he decides the best option is to give up his daughter and kill himself, both to protect Marin, and to ensure Junko can't use him or his money anymore. Bonus literal Tear Jerker moment when he leaves a message for his daughter in the future and it makes 2030!Marin burst into tears
