Lt. Cmdr. Jeffords, James Franciscus, an American serving with the Royal Navy Reserve, is assigned to Valletta, Malta, to command a small flotilla of Motor Torpedo Boats on a top-secret mission. He is allowed to bring his friend Chief Petty Officer Yacov, Reuven Bar-Yotam, a Jewish Palestinian, along.
Through scavenging spare parts from sunken craft, the battered flotilla cobbles together three seaworthy boats. Jeffords' objective is to destroy a former Italian submarine base in Augusta, Sicily, that now houses German Fritz X glide bombs—weapons that have devastated British shipping. The bombs are stored in submarine pens carved into a mountain, making an aerial strike unfeasible. It falls to Jeffords to devise a plan that can succeed under these constraints.
Off duty, Jeffords meets Alison Ashurst, Elizabeth Shepherd, the wife of his commanding officer Commander Andrew Ashurst, Ronald Allen, whose father is the Admiral who sent Jeffords to Malta, Moultrie Kelsall. Initially, Jeffords refuses Alison's advances, but during an air raid they share a kiss. After returning with a captured E-boat, he finds Alison waiting in his bed, and the moment implies they sleep together.
Jeffords then undertakes reconnaissance of the base with the help of the Sicilian Resistance. The mission is successful but costs the lives of his Resistance escorts; the Italian guide had been arrested earlier, complicating the operation.
Seeking a disabling strike, Jeffords hatches a plan to capture a German E-boat in a manner reminiscent of Ian Fleming's Operation Ruthless. By sending a false radio message that General Alexander's airplane has gone missing, Jeffords and his crew pose as survivors and lure a German boat to pick them up. They use the captured craft as a Trojan Horse to slip into the harbour, with the rest of the flotilla following once the Germans lift the boom gate. Jeffords and two others descend in scuba gear to swim through tunnels and plant explosive charges. However, by the time the charges are set, the MTBs and the E-boat depart, leaving Jeffords and his companion behind, as implied by the narrative. After returning with a captured E-boat, Philip Madoc the 'E' Boat Captain, Jeffords finds Alison waiting in his bed, and the moment implies they sleep together.
Back in Malta, Alison greets Andrew and Jeffords; Jeffords departs quietly, and it is suggested that Andrew and Alison will attempt to make their marriage work.
The historical backdrop: the Allied invasion of Sicily takes place in July 1943.