The Marie Elena is a pirate ship docked in the Waterfront District of Imperial City. The pirates around it will attack if an attempt to board is made, "stealing" or simply looking within the containers near the ship, or if they catch anyone on the floor or in the 'Captain's Chest' if the three aggressive pirates are dead. Either pick the lock or kill the captain in the quest "A Watery Grave" and take the captain's key.
The crates on the dock next to the pirate ship, and next to the gangplank, have a special status — as do the pirates. Because they are pirates, taking their goods, or even (in most cases) attacking them, is not considered a crime in the Imperial City.
For this reason, the 'theft' icon will not appear when one points at the crates; be warned, however, that the pirates will consider it stealing! Unlike the vast majority of item thefts in the game, one can sell any items looted from the pirates' crates to merchants. However, be aware that the count of "Items Stolen" in the Journal may go up.
If the Hero approaches the ship (but does not board it), First Mate Malvulis will engage the player in a conversation, warning to not enter the ship. True to her word, even touching the planks to board it will make the three pirates hostile. Despite her threat, characters can be seen walking on the ship with no consequences.
In the quest "A Watery Grave," the Hero must trespass to kill the captain. Killing (or provoking) the pirates or hiding in an open crate are methods to board the ship. If the option to hide in the crate was chosen, the Hero must start from the very bottom of the ship and avoid the occupants to reach the captain.
If attacked by the pirates, one can legally defend oneself, and any nearby city watch guards that see the assault come to the Hero's aid. So, wait until a guard is nearby before approaching the ship. After killing the Captain in his cabin, there will be two pirates coming into the cabin afterwards.
The pirates may do nothing and only utter snide comments if items are taken from the crates.