Against her better judgment (and ours), Charlotte sets out on a journey to America aboard the Seahawk, a ship captained by the seemingly charming Andrew Jaggery. Charlotte receives several warnings to not get on the boat, so we know that there will soon be some kind of drama coming our way.
One of the most important conflicts in the novel has to do with who will captain the ship. In other words, who's best fit to lead the small society of the Seahawk? Cranick and the crew try to dethrone Jaggery during the first mutiny, but Cranick gets killed and Zachariah is beaten within an inch of his life. Clearly, a violent upheaval driven by personal revenge isn't the way to get things done around here.
After the mutiny, the captain withdraws his protection of Charlotte, and she begins to live like one of the crew. Things on board were already tense, but Charlotte's gender bending aggravates Jaggery's already cruel behavior. Meanwhile, Charlotte becomes increasingly petulant, spitting at the captain's feet and threatening to take him to court in Providence. That rebellious behavior won't be tolerated for long, though. Something's gotta give.
Talk about an escalating situation! In the midst of the storm, Mr. Hollybrass is found with a knife in his back. The captain then charges Charlotte with his murder. (Talk about injustice!) Everything is coming to a boil here, as a showdown between Charlotte and Jaggery for the crew's loyalty (and control of the ship) seems unavoidable. Not to mention that Captain Jaggery's methods are starting to resemble madness.
Charlotte endures the show trial put on by Captain Jaggery, in which he argues that Charlotte's gender bending is unnatural and hence she's the one who murdered Mr. Hollybrass. (How's that for logic?) The men don't speak up for her, since they think Zachariah (who's still alive and hiding in the hold) is the one who actually murdered Hollybrass. Their silence protects Zachariah, though it condemns Charlotte to hang. The injustices inflicted upon Charlotte just keep piling up.
Charlotte and Zachariah realize that the captain murdered Mr. Hollybrass and stage a second mutiny. Captain Jaggery and Charlotte face off on the deck, and the captain is plunged into the sea by the movement of the ship. (Kind of neat – and convenient – that it's the ship itself that, in the end, does away with the captain.) Order is at long last restored to the boat, and Charlotte becomes the new captain of the ship.
Back in Rhode Island, Charlotte's father doesn't believe that her journal is factual. What's more, he actually goes so far as to burn the book. Unable to accept the mores of nineteenth-century society, Charlotte decides to return to the Seahawk.