On the night before his family moves from Danvers back to Salem, six-year-old Nat Bowditch tries to stay awake so he can work a magic spell by the power of the new moon. He desperately wants to change his family’s luck, which turned sour four years earlier, at the beginning of the Revolutionary War, when Father’s ship sank. Although Father’s luck seems to have improved when he buys an expectation on privateer Tom Perry’s next voyage, Perry’s death at sea quashes that hope.
Despite the mathematical genius Nat demonstrates at Master Watson’s school (drawing the attention of some of Salem’s best-educated citizens). Father withdraws him at the age of 12 and contracts him to an indenture in the chandlery (ship-outfitting business) of Mr. Ropes and Mr. Hodges. Unwilling to become “becalmed” like older employee Ben Meeker, Nat continues his education on his own, learning everything he can from conversations with men like the Revered Dr. Prince, Dr. Bentley, and Captain Samuel Smith, and from reading books he borrows from Mr. Ropes and the Salem Philosophical Library. It’s during his apprenticeship that he first befriends Elizabeth Boardman, and his favorite sister, Lizza, dies in an accident.
When his nine years of service in the chandlery have ended, Nat finds work with Dr. Bentley and Captain Gibaut on a survey of Salem; this leads him to an invitation to serve on the Henry under Captain Henry Prince. As second mate and ship’s clerk, Nat demonstrates his own navigational brilliance and begins to teach the common sailors how to navigate “by book,” or by using astronomical readings to calculate a ship’s position at sea. He also uses the French he learned during his apprenticeship to act as Prince’s translator in port. On the voyage home, Nat finds the first of many mistakes that mar the current navigational tables, and he figures out a newer, simpler, and more accurate way of taking lunar readings, thus improving the accuracy and safety of navigation overall.
Nat returns home to news of family tragedy; his sister Mary’s husband David and David’s entire crew died at sea. But this doesn’t stop Nat from sailing again with Captain Prince, this time on a record-breaking voyage halfway around the world to Manila. On this voyage, Nat proves his navigational skill when he guides the Astrea through the treacherous Sunda Strait with “book sailing.” And he meets, begins to teach, and ultimately befriends sailor Lem Harvey, whose tempestuous, aggressive nature calms when Nat’s navigation lessons give him a new outlet for his energies.
Soon after returning to Salem, Nat proposes to his childhood friend, Elizabeth Boardman. He learns that Lem Harvey has used his navigational education to sign on as an officer—second mate—on a smaller ship. And soon, Nat sails once more under Captain Prince, this time to the Mediterranean. Tragically, news reaches Nat on this voyage that Elizabeth has died of consumption (tuberculosis). When he returns to Salem, Nat throws himself into the writing of the world’s most comprehensive and accurate textbook of navigation to escape his grief. Eventually, he falls in love with and marries Polly Ingersoll.
A lifetime of losses to the ocean—his brothers Hab, William, and Samuel; his brother-in-law David; his wife Elizabeth’s father; and apparently even Lem Harvey—make Nat cautious about returning to the sea. He becomes a capitalist instead, investing money in a sealing ship, which unfortunately sinks. Then, Harvey miraculously returns. Feeling that his book will gain a wider reach if he can call himself a ship’s master, Nat takes the opportunity to command his own ship, the Putnam, as captain on a voyage to Sumatra for pepper.
On the way home, Nat finds himself beset by almost continual storms that delay his progress. When the storms finally clear and the ship should be practically in sight of Salem Harbor, it becomes lost in a thick fog. But, using a combination of “book sailing”—the last good sighting he got, 72 hours before landfall—and dead reckoning (tracking the ship’s position by monitoring its speed and tracking that against time), Nat successfully brings the Putnam in through a fog in which no other captain would have attempted to sail. Triumphant, he returns home to the welcoming arms of his friend Lem Harvey and wife Polly.