It is after the Napoleonic Wars and Napoleon has been confined to Elba. At the opening of The Hundred Days, Napoleon has escaped from Elba and made his way to Paris to be received enthusiastically by over 600,000 French. Many of the King's armies flock to Napoleon's side as he prepares for another attempt at the domination of Europe. Troops from a number of allied countries march to join up and stop Napoleon before he is able to regain his former strength.

On a second front, thousands of Muslim mercenaries gather to assist Napoleon's efforts by thwarting the Russians and Austrians from joining other forces bent on stopping Napoleon. The Muslim forces support Napoleon because of his alleged conversion to Islam while Napoleon was on campaign in Egypt. However, because the Muslim forces are mercenaries, they are unwilling to move against the Russians and Austrians without a guarantee of payment. Sheik Ibn Hazm has agreed to finance the use of the Muslim mercenaries by Napoleon and has authorized a shipment of gold ingots as a sign of his good faith.

Meanwhile, Commodore Jack Aubrey and his close friend, Doctor Stephen Maturin are tasked with the mission of halting the shipment of the gold and/or intercepting the gold so it does not reach the Muslim mercenaries. Additionally, the small fleet which Aubrey commands is tasked with finding and destroying shipbuilding facilities that have gone into high gear to re-build Napoleon's navy. Aubrey is aboard his flagship, Pomone, and commands several other vessels, most of which have little wartime experience. Doctor Maturin's wife, Donna, has been recently killed in a carriage accident and Maturin is still suffering the effects of his grief. His young daughter is being cared for by Sophie Aubrey, Jack's wife, and by the widow Oakes, whose deceased husband served under Aubrey for many years.

In order to try to keep the gold out of the hands of the mercenaries, Maturin and Amos Jacob, a British agent and expert on the area, ride into the Atlas to find the new Dey and request his cooperation in not allowing the gold to pass through his kingdom. The Dey, who is an ardent opponent of Napoleon, readily agrees. Unfortunately, the Dey is assassinated and the Vizier, who is a Napoleon sympathizer, makes arrangements for the gold to be brought by a corsair galley through the Straits of Gibraltar. After rejoining Aubrey, the squadron makes it way back to their home base in order to stop the galley from delivering its goods. Surprise is successful and receives not only much praise, but a goodly sum of prize monies.

When Aubrey and his group return to their home port, they learn that Napoleon is defeated at Waterloo and the war has effectively ended. Aubrey is sent to survey and chart Cape Horn and the Straits of Magellan.