- The entire prologue and first chapter. Made very heartbreaking by Jenna and Cindy being separated in Chapter 2.
- A Squirtle (who would be Sammy) goes out of his way to try to rescue a stranger (who would later become his trainer).
- When Alyssa and Cindy start to get along. Their bonding scene includes them sketching each other in the dirt.
- Anytime a Pokemon egg hatches. Bonus points for five of them hatching in the same scene. Even more bonus points for being Cindy's offspring.
- Cindy and her brother, Quinn beginning to bond.
- After their fight, they get captured, and work together to bust out of their prison. After they succeed, they apologize to each other, and cuddle next to each other.
- Jenna coming to the rescue of Cindy, who she thought was a stranger, from Anonimo, who was giving Cindy a reminder of the past with a whip. Jenna's heart of gold shines through, even when it comes to those she doesn't know (or in the case of Cindy, doesn't realize they're related).
- And she later breaks out to rescue her again, having found newfound strength after realizing who Cindy is.
- Cindy and Alyssa reuniting after the former was kidnapped.
- The Century Golden Lights scene.
- Cindy forgiving Ty after he nearly killed her and their children while under the influence of the Malonix virus. Note that Cindy doesn't usually forgive other characters easily.
- Jenna comforting Cindy after the latter lost her temper during a play the others set up; she was still hurt about the Quiltuplets having been given away.
- Sombra's prayer. He is just asking for forgiveness, and just admitting how much of a douchebag and murderer he's been. It is really a significant mark in his character development.
- Amber forgiving Sombra. Keep in mind that he had nearly killed her and her brother. It's almost like the Cindy forgiving Ty thing above, except she's surrounded by her friends and family, who loathe Sombra.
- Chapter 125, just for being such a sweet portrayal of Cindy and Ty's relationship. It makes what happens a couple of chapters later really heartbreaking.
- Charlie telling Diana that the spotlight doesn't matter, and that she just needs to ask for a friend. After his apology for his harsh "Reason You Suck" Speech and Diana's forgiveness and her pointing out that she deserved it, she asks him to be a friend to her. He eagerly accepts.
- It gets better. They eventually fall in love, resulting in the Dratini twins, Minnie and Scales.
- Sombra thinking of Mantle as a little brother. Mantle's one of four Pokémon who never gave up on Sombra (the others being Celebi, Pelee, and Dynamite), but he's referred to as the nicest.
- Joey's Big Brother Instinct. Even though he screws up, you know you can rely on Joey to come to your aid when you need it.
- Tiffany's bond with her father.
- Charlie planning to give a bouquet of daisies to Diana. His sweet childlike nature just adds to it. However, you just want to give him a hug when Pelee and Dynamite make fun of him and burn the bouquet.
- Blaze's concern for Ivy when she disappears.
- Boomer doing all he can to protect Amber from the rockslide. It's a real Tear Jerker when he fails.
- After Blaze's Blue Fire Frenzy, the poor fellow is in a Heroic BSoD. Ivy takes someone's advice to reassure him that he doesn't have to go through it alone. The hug after their short exchange is just beautiful.
- Bonus points for the advisor being, of all Pokémon, Emma.
- Sombra's sheer joy at Amber's recovery.
Heartwarming / Cindy's Story