When Gibbs and Bishop first enter the ship the aircraft Carrier Enterprises' island is visible through the open hatch she was in port for the 48-month inactivation process that rendered her unfit for further military service (inactivation removes fuel, fluids, furnishings, tools, fittings and de-energizes the ship's electrical system) in preparation for her eventual decommissioning.
A drunken bar patron refers to Bishop as DiNozzo's daughter. Michael Weatherly was born in 1968 and Emily Wickersham was born in 1984. With a 16 years age gap between the actors, he could be old enough to be her father, though he would have been a teen-aged father.