Late in Zero's storyline, Rhinne breaks from Will's control and tells him that even though she is supposed to eradicate any sources of corrupted time, including Zero, her motherly instinct to bring no harm to her children will always prevail. In the final chapter, it's followed up by Alpha and Beta's first act as the Transcendent of Time: Resurrecting Rhinne, in the process saving the Mirror World that they came to love as their home even though it was created to be their prison.
In the Cygnus Knight storyline, the Resistance refuses to provide assistance to the player and the children shun, boo, and harass any Cygnus Knight that approaches (like 10 Boogies) due to a failed promise in the past. However, after the player saves the local children (one of them being Ulrika Claudine's little sister) they agree to at least share intel. When the player bites off more than they can chew by getting themselves surrounded by the Black Wings, the Resistance swoops in to bail them out. While the Resistance claims that they were simply fulfilling their end of the bargain, this was the first time the Resistance and the Cygnus Knights put aside their differences in recent time.
The Grand Athenisium has you play the role of a lone mercenary 400 years ago who insists he's only in it for the money. But after finding a young girl named Erin, whose parents were killed by shadowy creatures called Omens, he takes her in and protects her like his own child despite her bratty behavior. He eventually teaches her to put value into her own life rather than go off on suicidal charges for revenge. In the end, she admits that he was closest she's had to a parent in years and begs for him not to die.
In the Explorer storyline Maple Island is ravaged by the Black Mage as an act of spite against the player. Even the Legends were unable to help them restore the island. However, it turned out that in the end, the spirit of camaraderie and adventure shared between the player and their friends was focused into the maple leaf that they took with them at the start of their journey, turning it into the Seal Stone that restored Maple Island.
At the end of Black Heaven, the player succumbs to Gelimer's poison and is on death's door. When all hope seemed lost, Cygnus decides to use the power of the last remaining Seal Stone to revive you, despite the fact that it is the last thing holding back the Black Mage's power. Her reasoning?
Cygnus: Hundreds of years ago, when the Dragon Mage created the Seal Stones, he made it the wish of the people: to save what's most important to them. And what's most important to us? The Seal Stone, or ''The Hero?"
In the Strange Stories event, the story of Edward, the Snow Child, has four endings. Three of them are bad, while the last is the only good one, as Edward is finally accepted by the villagers because he has saved them after transforming into a yeti, the very thing that made them fear him. They even find out that Edward was building a wall around the village because he wanted to protect them from the invading Yetis. The villagers see the errors of their ways and give him a nice home. In the end, you even get a nice shot of Edward and some of the villagers knitting. After everything the boy has gone through in the story, especially in the other endings, it just feels so nice seeing him finally being able to have a good, comfortable, and joyful life.
The Magatia subplot contains multiple different unsettling revelations, such as the truth behind the hidden passage and Magatia's usage of the Black Mage's alchemy, but includes a few warm ones as well; Humanoid A is the missing Dr. De Lang, who successfully made himself immortal and continues to love Phyllia and Keeny despite having no memories. You manage to cure Keeny of her illness, clear De Lang's name, and can tell Phyllia of what her husband was trying to do in the end.