This is part of the quest “Last Voyage of the USS Constitution” which will be triggered upon talking to one of the Lookout robots near the ship.
NE corner of the second deck has a cooking station and footlocker that may contain 3 Fusion Cores.
Green trunk located in the NW corner of the second deck.
In the 2nd level, the room to the SE near the bow of the ship has an unlocked safe. The 3rd Deck has a Master-locked room, Chem station, and weapons workbench.
In the Captain’s Cabin, there’s an issue of U.S. Covert Operations Manual on the corner round table to the left, from the doorway. There's also a stealth boy in the cabin as well.
If you helped launch the ship, it will relocate on top of a skyscraper. You can access it by riding two elevators in the building it’s sitting on. After visiting the ship again and talking to the captain, you’ll get the title “Honorary Lieutenant” and access to the captain’s quarters below.