- The Pirate Captain reconciling with his crew during the climax.
- The very end. "Welcome back...Captain."
- Then they HUG.
- The moment when the whole pirate crew forms a chain on the sinking ship to save the Pirate Captain and Polly from hitting the turbine's blades. It's even lampshaded, with the Pirate with Gout calling this their "most unexpectedly heartwarming adventure ever."
- In chapter three of the book, The Pirate in Green lets the Pirate Captain know that he's planning to get a tattoo of his face with him saying "Scurvy Knaves" on his upper arm and he wants to know if he's OK with it. The Pirate Captain is left speechless.Pirate Captain: Of course...I...ah...I don't know what to say.Pirate in Green: Are you okay, Captain?Pirate Captain: Yes...it's just this, um, ham. It's very spicy and it's making my eyes water.
- Which makes it heartwarming in the movie since the entire crew has The Pirate Captain's face as a tattoo on their body, with Pirate with a Scarf even saying that they got it because they adore and love him.
Heartwarming / The Pirates! In an Adventure with Scientists!