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Why did one of the U.S. Navy’s most advanced subs return to port with a pirate flag?

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 vessel 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 Carter, according to photos posted in April, also flew the Jolly Roger returning from its last patrol.

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. Cmdr. Max Horton, sank the German battle cruiser Hela, according to Richard Compton-Hall in his book “Submarines at War 1939-45.” Upon his return to port, Horton raised the iconic pirate flag, signaling he had 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, 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.”

Britain's Royal Navy has released a series of futuristic submarine concepts which mimic real marine life-forms and radically change the way underwater warfare could look in 50 years. (Video: Reuters)

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 sank 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 after 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 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. U.S. submarines, operating mainly in the Pacific, also flew their own battle flags upon returning from patrols. These pennants were unique to the boats but served the same purpose as the British Jolly Roger.

After World War II, the black 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 a U.S. submarine return home observing 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 that 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 probably splice undersea cables all while using specially outfitted thrusters to almost hover off the seafloor. One of the Seawolf class’s namesake subs participated in the Cold War-era operation Ivy Bells, in which U.S. submarines tapped Soviet underwater communication lines.

This post has been updated.