“The rumors are that the Navy's newest nuclear sub, the USS Jimmy Carter, has been designed for spywork, with a "special capability... to tap undersea cables and eavesdrop on the communications passing through them," according to the AP.”
ST6 is under the command of SOCOM, they do have the directorate to do clandestine work. To the degree that this article reflects any reality, it's also plausible that a partner in SOCOM (TFO/ISA) or an agency would be along for the ride to do anything specialized.