The narrative opens on a motionless sea where Captain Tom Lingard's swift brig is becalmed off the arid heights of Carimata. Lingard, a legendary figure among the islands, is secretly committed to restoring his native friend, Prince Hassim, and Hassim's sister Immada, to their rightful power in Wajo. His plans are abruptly complicated when a British yacht strands upon the Shallows, carrying passengers including the wealthy Mr. Travers, his enigmatic wife Edith, and their companion d'Alcacer.
Lingard recognizes that the presence of the yacht—and the official rescue missions it will provoke—threatens to destroy the delicate political balance he has spent years arranging with the local chieftain Belarab and the treacherous Tengga. Belarab rules a hidden inland settlement known as the Shore of Refuge, a sanctuary for outcasts where Lingard has built a fortress of arms and stores inside the hull of an abandoned schooner. As Lingard strives to keep the yacht's crew isolated and safe, his growing, unspoken bond with Edith Travers deepens amid the gathering storm of native intrigue, betrayal by Tengga, and the arrival of armed Illanun pirates led by Sherif Daman.
When Mr. Travers and d'Alcacer are kidnapped from a sandbank, Lingard is forced to choose between the completion of his life's great political mission and the immediate preservation of innocent lives. The story moves toward an inevitable collision between Western civilization and the archaic, fierce loyalties of the islands, leaving Lingard to face the ruins of his grand design.