As we learn more about Safina over the course of the game, it turns out that she’s not the great big sister that Maritte thought she was. She’s both directly and indirectly hurt people - including her friends - mostly by keeping secrets from each of them, and didn’t even tell anyone except Pertisia that Maritte even existed. In the end, Maritte isn’t ready to forgive her.
Gilda’s theme song at first sounds like she’s bragging about how she wants to be the best, but if you pay more attention to the lyrics, you’ll realise it’s actually about her insecurities and believing she must be better than everyone else because of how bad she was at magic before she got her lightning powers. Whenever you defeat her, she gets upset about it, feeling less confident in herself. One of the students tells you that her attacks become weaker when she has less HP, which is true even after she joins the party.
The flashback in the Ruins of Old Ikenfell, where Aeldra and her friend's attempt to stop the Dark Fold resulted in everyone but her being killed by it. She used their souls to imprison it, and is shown standing at their graves in the school's cemeterey.
Shortly before the final level, it's revealed that Pertisia was badly hurt by the Unseen, giving her scars on the left side of her face and damaging her eye, explaining why she had a panic attack when the party had to use the Unseen's area to get to the Snatcher's Lair earlier.
The Reveal of Aeldra's true nature. It turns out that she suffers from crippling PTSD due to watching all her friends and comrades die against the Black Fold, and in her despair she not only used Blood Magic to artificially remove her negative feelings regarding her final battle with the Black Fold, but also sealed away the Sapling because she feared that letting the seasons of magic change would mean having to forget her friends' sacrifice. At the climax, when the party confronts her, the earthquakes destroy the cauldron, causing all her memories to flood back into her and causing her to suffer a darkly realistic psychotic break where she genuinely believes that she's back at the final battle where she lost everything and begins lashing out at anything and everything.
The final boss fight against Ibn Oxley, who loses control of his powers after Bax gets badly wounded, believing him to be dead. The last half of the fight has him turn into a shadow monster, with sad piano music playing, and a slower version of said music plays during the last phase, where his attacks don't even deal that much damage, and he almost looks like he's crying. It makes you almost feel bad for fighting him, but you have to in order to save the world from destruction.
