The Ghost Pirates is the testimony of Jessop, the sole survivor of the Mortzestus, a merchant sailing ship already considered unlucky when he joins it in San Francisco. Hodgson's setting is unusually disciplined: almost every supernatural event occurs through the real machinery of a working ship—masts, yards, sails, ratlines, braces, the wheel, and the dark water alongside.

The escalation is the novel's great achievement. A lone figure climbs from the sea; shadows move where no sailor should be; men appear high in the rigging and vanish; lines and sails behave as if manipulated by invisible hands. The crew's explanations—stowaway, prank, accident, nerves—collapse one after another until phantom vessels surround the Mortzestus and ghostly boarders take physical possession of the deck.

Because Jessop understands only fragments, the book never reduces the haunting to a tidy mythology. Jessop's own theory suggests that the ship has crossed a barrier between material and immaterial worlds, but the final official statement can record only a loss at sea and one rescued sailor. The archaic dialogue and dense nautical terminology can be demanding; in return, they make the horror feel like something documented by working seamen rather than arranged for a Gothic set piece.