Why not just a common patrol of a SSN, departure, ASW and ASuw excercie, transit, mission : intelligence gathering in a lybian harbor with some excitement, periscope detection by a russian surface ship who chase the sub, trying to catch it with his anchor, the ship sail so fast that the crew did not retreeive the anchors (this really happen in the 80 aboard a french SSN), you can continue with a evading chapter (surface ship, airborne asset and maybe a russian sub) and finish with a return to home port.
Not very complicated, without conspiracy, a fool XO or a terrorsit attack and theft of a sub, just real life.
