| I should have been the one to fill your dark soul with liiiiiiiiiiight! |
In the Captain's Room, grab the Staff of Hermes from the statue behind the captain's skeleton. The ship will sink, and try to take Dante down with it. Fortunately, Dante doesn't die that easily. The door won't work now, so swim through the open grate by the floor next to it to get out.
Kill the two Blades to unlock the sealed door. Kill the Blades in the hold of the ship, and swim towards the top to find the stairway to the next area. You're right below the deck now, but make a detour down the stairs right where you found the Needlegun to grab a Blue Orb Fragment. Kill the blades for some more Red Orbs or skip them, your choice.
Head back out of there and into the hold again. At the opposite end of the room is another stairway down. Swim through it and go deeper into the hold. There are some more blades here. Kill them or skip them. There is a hole in the bottom of the ship through which you need to go. Swimming through there will end the mission.