- After the two of you spend the day in Goldenwood Forest, Melia tells you that she's going to be going to Grand Dream City to be the Normal leader soon, and asks if you want to come with her. Considering you only met her that day, and that you've got nowhere to stay due to your mother Nancy's kidnapping, this was incredibly sweet of her.
- Version 7's title screen shows a random part of Maria's family portrait, which in its full entirety is just plain adorable◊. Unfortunately it becomes less happy when you see what happens next.
- Version 8 added a small scene in Teila Resort in which Tesla, after hearing from Melia about what happened to your mother, swiftly proceeds to fix a room for your character and makes it clear that she intends to adopt you. Why? Simply out of good will, since she doesn't want you to grow up without a parent. Too bad it gets interrupted and ends up in a shouting match between her and Amber.
- Meta example: Right as the release of Version 9 was drawing near, Jan's computer ended up breaking down, which luckily didn't stop development by a whole lot because he stashed everything he was working on in a cloud server. Still, since he suddenly had no work station and without any means to finish the game, he was forced to ask the community for donations with the goal of getting him a new computer... A goal that was reached in less than a week. His "Thank You" post in the forums really sells it all.
- During the Amethyst Garufa ruins subplot, after April gives the Phase Dial to the Solrock and Lunatone, they inexplicably start dancing. In what's a really adorable moment, April shrugs and dances along with the player, talking about how fun dancing is.
- After you fix things in Goldenleaf Town, talking to the residents has most of them apologising for their earlier actions and generally being much friendlier.
- The good ending of the bad future part of Version 10: Amber, Mosley, Kenneth and Tesla admiring the new world, talking about how they're going to make it a better place for everyone.
- Completing the Lost Camp sidequest in Version 11 treats you with a scene of Mosely, while sad that Maman passed away from her illness, vowing to turn over a new leaf and to continue her job in the Lost Camp to take care of every single child you found through the quest. She proceeds to thank you for helping her out so much through the entire game, gifting you a Starly she raised from an egg, and giving you the largest relationship point increase in the entire game (An astonishing +999).
- Anastasia stole the still Taken for Granite Venam from the Hospital of Hope of her own initiative to bring her to the Spring of Rejuvenation, seemingly hoping that it would be able to heal her along with Allen, Alice, and Melia. It worked, and she's fine again. Really makes you wonder how much of her Tsundere attitude is genuine...
- Erin, Melia, Allen, and Alice all reuniting/meeting for the first time. Up to this point in the story, Melia has lost her adoptive father and learned that she has been lied to by Spacea and Tiempa, and been targeted for the "light" in her. Allen and Alice both spent potentially most of their lives in the Unown Dimension, to the point that Alice didn't realize the real world wasn't the same place and goes sorta crazy for a bit. Allen had to learn and adjust to this whole thing, as well as the fact that his sister was pulling a More Than Mind Control on him. And Erin grew up in a Friendless Background and was apparently neglected by Souta to a degree, enough that she was planning to kill herself. And, well... even if it's only the start of things, they've all got each other now, at least.
Heartwarming / Pokemon Rejuvenation