- Cute normal form Shaymin, when it's not being a Jerkass towards Ash anyway. Though Shaymin at least undergoes some Character Development, leading to it and Ash becoming genuine friends.
- Shaymin reviving Giratina with Aromatherapy. It's nice seeing Shaymin finally overcome its fear of Giratina.
- Shaymin's farewell at the end of the movie.
- Post credits, when we see Zero pulled out of the Megarig, Newton looking pretty upset, but once he sees Zero, his face softens, and he outreaches his hand to help him out.
- The credits show cute scenes of Delia Ketchum, Brock's family and Dawn's mother receiving the Gracidea flower bouquets that Ash, Brock and Dawn sent them.
Heartwarming / Pokémon: Giratina and the Sky Warrior