The Stonington, a whaleship from New London, Connecticut, is sailing a course for home after being at sea for more than three years. When it pulls into San Diego, California in September 1846 for food and supplies, the crew learns that war has broken out between the United States and Mexico. The town is under siege by Mexican forces, leaving the US inhabitants no escape route but the sea. In response to their desperate situation, the Stonington's captain allows them to take refuge aboard his ship. Thus begins the first step in what would become the Stonington's months-long tour of duty as a member of the US Navy's Pacific Squadron.

Using the logbook of the whaleship Stonington together with other primary and secondary sources, historian Peter J. Emanuel, Jr. tells the story of a whaleship unlike any other in the annals of whaling. Readers with an interest in maritime/naval/military history, as well as those who just enjoy an exciting adventure story, will sail along with the Stonington as it assists in the retaking of San Diego, then serves as a supply ship, a troop ship, and even a gun ship for the US Navy. The captain and his crew interact with central figures in the US war effort in California, including Commodore Robert F. Stockton, John C. Frémont, Ezekiel Merritt, and General Stephen W. Kearny.

A series of harrowing events unfolds when the US Navy releases the Stonington and the ship resumes its homeward course. Mexicans capture the captain, and the first mate must decide whether to attempt a rescue that could jeopardize the entire ship. The ship must sail around Cape Horn through one of the most dangerous waterways on the planet. Lightning strikes a crewman high in the rigging and, after managing to pass him down safely to the deck, his crewmates keep vigil as he struggles to survive, all the while hoping that they will get back home.