- Zhamo never hating Eluca even though she executed his parents, and would've killed him too.
- Olgar's character development. In the first ending, where he and Vahti have to spend another 10,000 years generating a new human race, his goal is to fulfill Zhamo's utopian dreams for him. This being after the Ark reaches the end of its lifespan.
- Escher finally being forgiven by Musiea. Even before then, Escher verbally giving her the time to forgive him.
- Olgar choosing his wife over humanity, even if it meant the destruction of hundreds upon thousands of Timespaces (pretty much, universes and their multiple timelines.
- Wait, what?
- Mana using her own lifeforce to defeat the Executioner so that it wouldn't destroy Ayuta (Jerk Ass that he was in Olgar's story). Then, Ayuta's suicidal charge at The Agent when he (it?) abducts her.
- Theia's clone (with Vahti's looks and memories) putting her feelings aside to help Olgar get back to "the real me", as she puts it.
- The end of the game. Theia does still have a heart...
- Escher promising Musiea, a.k.a. Aida that he would find her after they were sent back to their original times before they were summoned.
- Every character on their death scenes. Except maybe Alto and Garrick.
- In Omega...
- Olgar (Dante), according to Word Of God, sees his son-in-law Vieg (Olgar in the main story) as the only person he can depend on. (He'd never mention it to his face)
- Yorath's search for the truth, and his eventual Face Heel Turn.
- Considering those two, Dante taking Yorath's ultimate attack (Divine Diversion) head-on, and in a scripted battle, showing just how much of a Determinator he is.
- How all of the Ark's participants gather round for Vahti giving birth to Ohm, though Cyllis's behavior, in hindsight, is rather...scary.
- Ayuta simply wanting for his partner, Kushina to be happy, despite the shame he'd have to go through to be with her, as she wishes. They come from a place steeped in feudalism. Aaaaand...then she dies in his arms while facing Cyllis and Yorath.
Heartwarming / Chaos Rings
This game is full of them. For example: