The story follows Jack Aubrey as he takes command of HMS Leopard on a mission meant to reach Australia, and occurs prior to the War of 1812.

Critics praised the novel's “literate, clear-eyed realism” at initial publication,[1] as well as the stirring naval action in the cold southern ocean as the Leopard is chased by the Dutch ship.

[2] Having recovered financially in The Mauritius Command, Captain Jack Aubrey is expanding his home and has paid off his mother-in-law's debts, and his wife is no longer pinching pennies.

Despite his comfortable pay while serving in the Fencibles office, he is still frittering away his fortune with foolish business endeavours, and Stephen Maturin suggests that Jack's tendency to assume honesty in others is getting him cheated at cards.

Stephen learns that Diana Villiers has returned from America, unmarried, but when he calls upon her he only finds a letter explaining that her young American friend Louisa Wogan has been apprehended by British authorities and questioned as a spy.

Sir Joseph Blaine explains to Stephen that Mrs Wogan will be carried aboard the Leopard as a prisoner, along with two dozen other convicts to disguise the nature of the charges against her.

Partly to prevent Stephen's laudanum addiction from compromising his work, Blaine assigns Maturin to the voyage to watch Wogan, hoping that by doing so he may uncover American secrets.

Jack orders their conditions be improved to meet naval standards but an outbreak of gaol fever nonetheless spreads from the convicts to the seamen, killing most of the male prisoners and 116 of the ship's crew and leaving the Leopard severely undermanned.

The Leopard encounters the Dutch ship before reaching the Cape of Good Hope, but Jack cannot risk a confrontation with the much larger and fully manned Waakzaamheid.

He repels a boarding party with grapeshot during the night and nearly escapes his pursuer, but the Dutch captain eerily predicts Jack's every move and blocks his route to the Cape.

The Dutchman chases them south into the Roaring Forties for five days, where the waves and wind increase, and the ships finally engage in dangerously high seas.

Desperate to save the ship, all hands work the pumps continuously for days and rush to fother a sail to stop the leak.

Making adroit use of anchors and a jury-rigged rudder, Jack navigates the ship to safe harbour in a bay of the remote, uninhabited, and poorly charted Desolation Island just as a storm approaches.

After a few days a whaler arrives in the bay: it is the American brig La Fayette, returning to the island to resupply with the edible cabbages growing on shore, which they need to combat scurvy.

While Jack is distracted by the ceremony of setting the new rudder in place, Stephen and Barret Bonden watch from a distance as Herapath and Wogan slip away in the night to board the whaler.

At Craddock's for cards At Ashgrove Cottage dinner On the Leopard On the American whaler, the brig La Fayette of Nantucket, Massachusetts Kirkus Reviews noted the "usual action" present in Desolation Island compared to other nautical novels, and praised O'Brian's "literate, clear-eyed realism", which may broaden the audience for the novel beyond the usual readers of a story set on sailing ships.

"[2] The Leopard stops for water and fresh supplies in Saint Jago, one of the Cape Verde islands, west of Senegal and in Aubrey's time a colony of Portugal.

O'Brian based the account of the near-sinking of the Leopard, after striking an iceberg, on an actual event involving HMS Guardian and her commander Edward Riou in 1789.

They journey to the Underworld, below the equator, to the high southern latitudes, experience epic trials, and achieve redemption at Desolation Island.

[6] Desolation Island differs from the prior novels in the series in that the main characters are not back in England or safely on their way by the end of the story.