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 Pirate Captain and Polly from hitting the turbine's blades. It's even lampshaded, with one of the crew calling this their "most 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.