The True Confessions of Charlotte Doyle opens in Liverpool during the summer of 1832 where Charlotte, accompanied by Mr. Grummage, is about to board a ship called the Seahawk. The other two families who were set to join her on the voyage don't show up, for whatever reason. Against her gut feeling, and the warnings of a couple of the crewmembers, Charlotte makes the journey anyhow. Also important: before the boat leaves the dock, Charlotte sees a shadowy figure steal aboard the ship. (Never a good sign.)
On board, Charlotte meets Captain Jaggery, a fastidiously dressed man with impeccable manners. She likes him immediately, and he asks her to be his eyes and ears (read: he wants her to spy for him, not undergo complicated surgery). She also meets Zachariah, a lowly black cook who's generous and kind, but whom Charlotte doesn't think she should associate with, as she believes him to be her "inferior" (5.1). Zachariah tells Charlotte about Captain Jaggery's misconduct on the Seahawk's last voyage. Apparently he beat one of the crewmembers until the poor guy lost his arm. Harsh? Yes. But Charlotte doesn't really believe it. Around this time, Zachariah gives Charlotte a knife called a dirk, a weapon with which to protect herself. He also gives her a set of sailor clothes (a miniature pair of pants and a shirt), which she doesn't wear, but stows in her cabin nonetheless.
One day on the boat, Charlotte has an adventure when she's attempting to retrieve her trunk of clothes from the steerage. All alone in the top cargo of the ship, she spies a grinning head at the foot of the ladder. Upon closer inspection, she realizes it's a grotesque face carved into a brown nut. Who put it there? Was it the stowaway she saw climbing onto the ship? She convinces herself it was probably nothing.
As the voyage continues, Charlotte spends her time in her cabin or sometimes reads to the crew. One day, though, Charlotte overhears plans for a mutiny amongst the crew. She immediately alerts Captain Jaggery. Grabbing his guns, Jaggery heads for the deck where he and the crew dramatically face off. The mutinous crew is led by Mr. Cranick, the one-armed man who's back for revenge. (He was the stowaway Charlotte saw climb onto the boat that night.) Captain Jaggery shoots Cranick (ouch!), and then picks a scapegoat from the crew to punish for the mutiny. Jaggery chooses Zachariah, who is the only one of the crew who stands up to Captain Jaggery and tells him he's a cruel guy. For this, both Mr. Hollybrass (the first mate) and Captain Jaggery beat Zachariah mercilessly. When Charlotte attempts to intervene, she accidentally flicks the captain with a whip. He's so not thrilled about this, to say the least. Also a bummer? Zachariah appears to be dead. The crew holds a funeral for him and throws a tied up hammock out to sea, which Charlotte assumes contains Zachariah's body.
As the first part of the novel draws to a close, Charlotte attempts to apologize to the captain for hitting him with the whip, but he flat out rejects her. Feeling forlorn and abandoned, she decides she must take responsibility for herself and atone for her actions. Charlotte then dons the trousers and blouse that Zachariah gave to her and sets out to join the crew.
As the second half of the book opens, Charlotte is now a member of the crew. She climbs the masts and learns to use her knife just like the rest of the sailors. Meanwhile, Captain Jaggery harasses the poor girl to no end. He also begins to steer the ship toward a hurricane so that the ship can take advantage of the strong winds and make better time. Dangerous? Um, a resounding yes.
Eventually the hurricane strikes the ship head on. During the storm, Charlotte loses her balance in the rigging. As she is about to fall, she gets saved by someone who looks just like Zachariah… Is it a ghost? An angel? She isn't sure. After the storm, the drama builds even more as Mr. Hollybrass is discovered face down on the deck with a knife in his back. Yikes. No one knows who killed the first mate, but Captain Jaggery accuses Charlotte of the murder and sends her to the brig.
As Charlotte awaits trial, Zachariah visits her in her cell. He's not dead after all, but has been hiding down in the hold. (The hammock thrown into the ocean was a decoy.) Charlotte is sure happy to see Zachariah alive! The good times, though, are short-lived. Charlotte is taken from her cell, tried, and found guilty by the captain and a jury made up of the crew. Jaggery calls her an "unnatural" girl and uses a chain of faulty logic to convict her. The men on the jury don't speak up because they're protecting Zachariah, who they assume is the one who killed Mr. Hollybrass. The captain sentences Charlotte to death by hanging.
After the trial, Charlotte awaits her execution. She and Zachariah put their heads together and realize that it must have been Jaggery who murdered Mr. Hollybrass. They try to stage another mutiny, but Keetch, the second mate, rats them out. Apparently, he was Jaggery's spy all along. (Dang!) Charlotte and Jaggery then have an epic showdown on the deck. In the end, Jaggery falls into the sea due to the swaying motion of the ship. Zachariah declares Charlotte the new captain. (Though in name only – Zachariah really does most of the captaining. Sweet gesture nonetheless.)
The ship lands in Rhode Island, and Charlotte returns home where her family are completely shocked by her appearance and manner. She tries to befriend the servants, but with no luck. Charlotte's father reads her journal but doesn't believe any of the contents. He's most appalled by the spelling. (Seriously? Yes.) Soon after, Charlotte sees an advertisement for the Seahawk's latest departure in the newspaper. Deciding that she can't live in the stifling world of her spelling-sensitive family, Charlotte sneaks out of her house and rejoins the crew of the Seahawk. The first person she sees when she gets to the docks is, of course, Zachariah.