During the fighting between the Lost Boys and Pirates, Hook confronted Rufio in sword combat, and ended up killing him.
However, Peter Pan returns to save Sora before imitating Smee to trick Hook out to the deck, resulting in the villain being thrown overboard and chased into the horizon by the crocodile.
In the end, Peter is victorious but at the request of his children saying that Hook is only a spiteful man without parents who can no longer hurt them, spares the captain's life, and simply tells him to leave Neverland and never return.