I have just made my way to the waterfronts and saw the pirate ship. THen the pirates tell me that if i go on their ship they'll me. So, being the cunniving and intelligent Elf that I am I wait till the guard comes back towards us. As he does I step on the boat. The Pirates attack me and are in turn attacked by the guard who kills all three (with a little help from my bow).

Now I dont know what to do. Did this ship have a captain because I haven't seen him around. i've looted the ship. There wasn't much on it. anything interesting I could do with this ship?

You could live on the ship if you like. In the lower decks there are plenty of open top grain sacks (they are all safe storage).

The captain of the ship does not exist yet. If you do the Dark Brotherhood questline, he will appear for one of the quests. The fact that you have killed (or caused to be killed) his crew will not affect that Dark Brotherhood quest if you embark on that questline.

So. . . really the only impact is that are a few less folks on the waterfront to add atmosphere to the game, and you have unlimited access now to the Marie Elena.

Nice! A place to live. I have been searching for one. Nobody wants to sell me one and I can't make money because i have no place to store my stuff.
cheers!

Just a heads up...

Make sure you remove any loot you have stored in the ship before you begin the Dark Brotherhood quests. I had my things dissappear as soon as the quest regarding the ship was started. I think the ship "resets" at this point. Don't know if this has happened to everyone, or just me.

It has happened to me before.

I recommend getting the Drak Brotherhood quests done, before using the ship as a home.

cool thanks

glad to know the ship can be used as a house.