- Max offers Lucario some of his chocolate. Lucario (who's never had the stuff before) tries it, and likes it.
- When Lucario is able to hear Sir Aaron's final words through a Time Flower.
- After Jessie is eaten by the Tree's defenses, James is grabbed as well. Quickly thinking, he releases Chimecho (Cacnea was already out), so his Pokémon would not suffer his fate with him. From there on, Brock, May, Kidd, and Ash would call out all their own Pokémon as well, for the same reason.
- Ash seeing the painting of Sir Aaron now has Lucario beside him.
- Post credits Sir Aaron and Lucario split a bar of chocolate.
- Meowth reuniting with Jessie and James may very well be one of the cutest moments in the entire series.
- Ash: (thinking) No, Lucario isn't really gone.(speaking) Its Aura is with me!
Heartwarming / Pokémon: Lucario and the Mystery of Mew