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MrPlow writes:

Submitted via IRC for Runaway1956

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.

[...] 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.

Source: Why did one of the US Navy's most advanced subs return to port with a pirate flag?

Also:

The ominous Jolly Roger is an important part of submariner lore and conveys a clear message when it is flown atop a submarine's conning tower.

Source: Why The Navy's Top Spy Submarine Flew A Pirate Flag While Pulling Into Port

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