Inside the Captain's Room, make sure that you have all that you need from the God of Time, then grab the Staff of Hermes near the right side of the room. This item will be used a few missions from now. After the item is pulled, the ship sinks, so you must get out.

Swim through the ventilation hole to the right of the blocked door. You need to kill the two Blades to unseal the room and leave. Using the Needlegun is tricky.

Learn to fire, then move if you see the Blades pointing their hands at you. If you swim against a Blade while it is swimming at Dante, you can "stop" it in mid-water, and pump shot after shot into the Blade using the Needlegun.

Swim through to the next area, ignore the two Blades there and go through the hole in the hull of the ship and you will end the mission!