An image posted to a Pentagon media site and tweeted by Scottish journalist Ian Keddie, shows the USS Jimmy Carter, a Seawolf-class nuclear-powered submarine, returning to her home port in Washington Tuesday flying the American flag alongside the unmistakable pirate skull and crossed bones, known as the Jolly Roger.

The 450-foot-long boat is one of three in its class and is specially modified to conduct some of America’s most covert underwater operations. That fact alone – as Keddie points out – makes the appearance of the black and white flag significant.

The Jolly Roger’s presence on the conning tower of submarines goes back to 1914, at the beginning of World War I, when a British submarine, HMS E-9, commanded by Lt. Cdr. Max Horton sunk the German Battle Cruiser Hela, according to Richard Compton-Hall in his book “Submarines at War 1939-45.” Upon his return to port, Horton struck up the iconic pirate flag, signaling he had successfully sunk an enemy warship. As Horton’s kills accumulated, he began denoting them by affixing bars to the flag.

Ali Kefford, in an article for the Mirror, said that Horton’s decision to fly the black flag stemmed from insults made roughly 14 years before by British Adm. Arthur Wilson, the then-Controller of the Navy. Wilson said submarines were an “underhand form of attack” and that their crews would be “treated as pirates in wartime.” Wilson went on to say that the undersea boats were “weapons of a weaker power and can be no possible use to the Mistress of the Seas.”

At least one other submarine took up Horton’s tradition during the Great War, according to Compton-Hall, but it didn’t catch on in the Royal Navy until World War II.

In 1940, the submarine HMS Osiris, infiltrated the Adriatic Sea, a body of water that then-Italian Prime Minister Benito Mussolini said could not be penetrated. Once inside, the Osiris sunk the Italian destroyer Palestro. Upon its return to one of the British flotillas in the Mediterranean, the flotilla’s commander signaled to the Osiris that the submarine would fly a special recognition following its successful mission and that the Osiris was “not to come alongside until the identity signal is showing,” Compton-Hall wrote. A launch from the flotilla then delivered a package marked “JR” to the Osiris. Inside, was the iconic black and white pirate flag which the Osiris then proudly ran up its tower before reuniting with the flotilla. From then on, flotilla commanders awarded the Jolly Roger to submarines following their first successes. It was up to the signalmen aboard the underwater boats to ensure their flags were updated with the symbols that denoted their sinkings and patrols, according to Compton-Hall.

For the British subs operating out of Malta, flags were supplied by Carmela Cassar, a business executive who maintained a lace shop supplied by the city’s surrounding convents, according to Compton-Hall. Her flags were 12 by 18 inches and “beautifully embroidered.” When the submarines failed to return, her flags were sometimes all that remained.

While the tradition stayed mostly with the British submarine fleets, Compton-Hall writes that Allied submarines also occasionally flew the Jolly Roger. After World War II, the flag popped up sporadically, appearing on the Churchill-class HMS Conqueror upon its return from the Falkland Islands in 1982. During its deployment, the Conqueror sank an Argentine cruiser with two torpedoes.

So why did it a U.S. submarine return home flying an undoubtedly British tradition? Much is unclear. U.S. submarine activity is rarely discussed by the Pentagon, and the vessels operate in almost complete secrecy. While it’s unlikely the Carter torpedoed an enemy ship or fired one of its cruise missiles, the flag could represent the success of a more covert mission. The Carter can insert commandos, deploy unmanned submersible vehicles, and likely splice undersea cables all while using specially outfitted thrusters to almost hover off the seafloor. One of the Seawolf class’s namesake participated in the Cold War-era operation Ivy Bells that saw U.S. submarines tapping Soviet underwater communication lines.

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