After you've talked to Sam go to the designated area. Approach the guard shown in the screenshot. Toss a stone and lure him away from the Docks descent. Once the passage is clear, start going even lower.
Wait for the guard shown in the screenshot to move and follow him, while keeping a safe distance.
When he reaches the area shown in the screenshot, wait for the other guard to go lower. Go around the enemy on the chair on the right, behind his back. On the far right-hand side, there is a passage that will take you deeper.
Once there, squeeze past the enemy shown in the screenshot, behind his back, and go over to the left side of the cave. Wait for him to turn his back at the descent and go ahead. If necessary, toss a stone to lure him away from the descent.
Further on, toss a stone to divert the attention of the enemy shown in the screenshot.
Keep to the left of the cave and go past the corpses, and go ahead. You will reach the marked spot on the left side of the cave. From here, you will notice several enemies shown in the screenshot.
Get over to the left side of the cave, to end up behind the enemy on the chair (the screenshot).
After you go down, keep to the right, to get around the armored enemy (in the screenshot with the shield symbol over his head), behind his back.
When you reach the pier, jump into water and dive immediately. Swim over to the back of the ship and climb the ladder to get aboard. Sneak behind the guard right behind the crates on the left and kill him.
After the conversation, approach the man-controlling guard. Approach the pedestal and listen to the speech. Right after you regain control of your character, climb the pedestal yourself. Go over to the other side and go straight ahead. Take the first turn to the left and go through the door. Go past the guards and to the boat, which you need to take to leave the area.