You must track down Charles Lee. He will be at the red marker on the map in a graveyard giving a eulogy for Haytham. Walk along the left side of the graveyard and when you find an opening in the fence near the church, enter the graveyard. Approach Charles Lee to see a cutscene.
Afterwards, you'll find yourself being beat by some soldiers. When the man goes to swing at you, counter his attack. Fight off these few men and then when they are dead, you'll have to enter the graveyard for another fight. You must kill all of the marked mercenaries. It's best to start from the church roof and assassinate someone from there. Try to pick one of the tougher looking enemies to save yourself some trouble. Most of these enemies are pretty simple but there a couple of tricky ones so be on guard.
When you've dealt with them, make your way into the harbor and swim out to the ferry. To get aboard, you need to swim around the far side and find a rope to climb up. Climb up to the platform that is jutting out a little ways and hang down from it. You'll likely see a guard standing just about you and there will be a building to your left. Don't kill the guard and if he's not there, wait for him to come. He'll look out to sea for a little bit and then turn around to walk back. When he does, climb up to the top of the building on your left.
From this roof, look straight ahead (towards the back of the ship) and you should see another taller building with a guard standing at the top of the stairs attached to it. Wait for that guard to disappear and then make a dash for the building. Get up on the roof and try to stay there without being noticed. Stay on the side away from the guard behind the building. Wait for him to return to standing at the top of the stairs and then drop onto the marker to investigate. As soon as you've done that, get back on the building and disappear again.
From this building, jump back across to the previous building. Let yourself down the outside of the ship to the beams sticking out under the building. You'll see that there are now markers for people you can't kill and a ring indicating that you need to listen in. Climb up to the window and listen from just outside.
Now move along the outside of the ship and head to the right. Head to the back of the ship and hang by the brightly light windows but don't climb so high that you can be seen from the left. When the guards on the left have disappeared, climb up over the lip at the back of the ship and take up a corner cover position by the window you need to eavesdrop at. When you've listened in successfully, you'll be left with only two things to do.
You can kill the captain of the ship if you like to finish your constraints but this is tough to do or you can leave the ship. Probably the best bet for killing the captain is to return to the roof of the building in the middle and work from there. Remember that you can only kill a couple of guards to fit within the constraint so choose wisely. Kill the captain without getting caught and jump off the ship to freedom and you'll finish the mission.
