In 1941 Lieutenant Commander Jeffords (James Franciscus), an American serving with the Royal Navy is assigned to Valletta, Malta, to command a flotilla of Motor Torpedo Boats for a top secret mission. Jeffords is granted permission to take his friend Chief Petty Officer Yacov (Reuven Bar-Yotam), a Jewish Palestinian, with him.

Through scrounging spare parts from sunken craft, the battered flotilla is able to piece together three seaworthy craft. Jeffords' mission is to destroy a former Italian submarine base in Augusta, Sicily, that now contains the German's Fritz X glide bombs that have been taking a heavy toll of British shipping. As the bombs are stored in former submarine pens tunnelled inside a mountain, an aerial attack is unfeasible. It is up to Jeffords to determine how he will accomplish his mission.

Off duty, Jeffords meets Alison Ashurst (Elizabeth Shepherd) bathing in the nude; she turns out to be the wife of his commanding officer Commander Andrew Ashurst (Ronald Allen), whose father is the Admiral who sent Jeffords to Malta. Jeffords initially turns down her offer of having an affair but during an air raid they take shelter and kiss. Later, after returning with a captured E-boat, Jeffords finds Alison waiting for him in his bed. It's implied they then sleep together.

Jeffords first decides to make a reconnaissance of his target by being taken into the base by the Sicilian Resistance. Jeffords' mission is successful, but at the cost of the lives of his Resistance escort. The Italian officer who was supposed to guide him had earlier been arrested.

Jeffords schemes to capture a German E-Boat in a manner similar to Commander Ian Fleming's Operation Ruthless. By sending a false radio message that General Alexander's aeroplane has gone missing in a certain area, Jeffords and crew pose as survivors of the crash then capture the boat attempting to pick them up. Jeffords uses the captured craft as a Trojan Horse to penetrate the harbour, having the other boats in the flotilla follow his captured craft in once the Germans have lifted their boom gate. Jeffords and two others don Scuba sets to swim into the tunnels and plant explosive charges. Contrary to Jeffords' instructions, the MTBs (all of which are eventually lost) and the E-boat wait to pick him and his chief up.

After returning to Malta, Alison greets Andrew and Jeffords. Jeffords leaves silently, and it is implied Andrew and Alison will try and make their marriage work.

The Allied invasion of Sicily took place in July 1943.

• Hanover Street, a 1979 film starring Harrison Ford, whose plot includes a similar love triangle.

• Hell Boats at IMDb  
• Hell Boats at AllMovie
• Hell Boats at the TCM Movie Database
• Hell Boats at the American Film Institute Catalog