* This is literally what chapter fourteen is all about.
** And chapter eighteen, though it's more bittersweet about it.
* Mewtwo's feelings and loyalty for Mew, especially when it keeps him from doing things he knows can hurt her.
* The IntimateHealing portion of chapter two, particularly when you later learn the truth behind why Mewtwo agreed to take care of her and how Mew got into that condition.
** Thus, [[spoiler: Mew's bittersweet bond with the child]] becomes a TearJerker since you know what the outcome is going to be.
* Ho-oh leading the group prayer even though most of them were against the thought, Giratina in particular.
* Mewtwo and Mew becoming mates even after death.
* [[AwLookTheyReallyDoLoveEachOther The Legendaries comforting Mewtwo during his breakdown.]]
* Mew's departure from [[spoiler: the Spirit World]] where everyone she had known and loved came to wish her well. [[spoiler: She is even reunited with her mother.]]
* The reunion between Mewtwo and Mew even though it gives a HopeSpot before the final battle.