Before you execute the mission. You will have to plant a tracking device on the car. (This is optional, leaving the car alone does not affect your rating in any way) Go to the strip club and approach a stripper. She will then go out and distract the guard from your sight. Plant the tracking device, and stay away from the car. Now this is where the real mission start:
There are 3 ways to do this mission:
Assassinating Boris on his ship
This is arguably the most silent way to assassinate Boris. First of all, disconnect the satellite link, so that a guard come to fix it. When he does, take care of him and pick his clothes. Or if you don't want to take the risk of the guard waking up, you can try to sneak into the police station and take the Police outfit in the wardrobe without getting spotted by the cops.
Head for the second warehouse door and pick the lock. Do not let the cops see you. After that, get inside the warehouse. Here, you can choose to kill one of the henchmen and take his clothes, or sneak to the upper floor and gain their uniform. Remember, killing one enemy is tolerable to maintain your Silent Assassin rating.
After that, go straight to the ship. At the ship, you have the option to disarm the bomb that was in the cargo loads or going straight to Boris himself. If you choose to disarm the bomb first, go downstairs and check your map for the car that was planted by the GPS tracker. Open the trunk and disarm the bomb. If you want to attack Boris directly, go and follow him all the way until he reaches his room. Inside, kill him, and leave before the SWAT team attacks. Since Boris is already dead, he will be unable to armed the bomb, so there is no worry if you don't disarm it first.
Finally, equip the Police uniform, and get out of the police station. Head for your exit to complete the mission.
Go to the main gate guarded by policemen. Again, disconnect the satellite link, so that a guard come to fix it, knock him out, and pick his clothes. However, if you don't want to do so, another way is to wait for the police to come out from the office and walks further. Once the police has gone away, go to the nearby SWAT occupied warehouse.
Once inside the warehouse, go hide behind to some objects and prepare the sedative syringe to sedate the squad member. Before sedate the squad member, make sure he is not looking at you just before you begin to sedate him, once you manage to get behind his back without detected, quickly sedate him and take his cloth including his assault rifle. Drag his body inside in case you sedate him outside the room.
After you done, go through the door where the squad members line up for an assault. If they haven't line up, you can choose line up first if you do so. If they already line up, you can also choose to stand behind them or walk to the empty space and then crouch.
As they told you and the rest to move, just move behind them. When they stop behind the container, you need to stop and crouch near them, if you want to finish the mission quickly, just skip the plan that mentioned and just raid the ship directly.
[If you think you have God level shooting skills and timing, go to the side of the harbour and aim your Silverballers at the corridor with the place where Boris' cutscene would play. You can aim in first person for more precision. Now as the gunfight happens on the ship, keep your eyes peeled. Boris will soon run through the corridor, left to right. Shoot him in the head, holster your gun and escape by the tunnel. Of course, you won't get Silent Assassin if you have already killed any enemies.]
Once on the ship, whether if you with the moving squad or not, try to keep you distance between you and the terrorist guards below to prevent them from shooting you. If you want to achieve silent assassin, try not to shoot the terrorist guards below while you are moving.
As you move at the back of the ship, climb up the ladder and climb to the next ladder at the right side of the ship. Avoid taking the stair at the left side of the ship as two of the squad members are guarding the door. Wait for the cutscene to play out (don't skip) before entering the cockpit. Once inside the ship's cockpit, take out the fiber wire and strangle Boris. After you killed him, take the detonator and get out of the ship. You can choose to disarm the bomb or escape with or without the assault rifle. If you want to disarm the bomb, go below the ship and open one of each container to find the car that has the bomb in it and disarm it. Before disarm the bomb, make sure there are no terrorist guards patrolling down there.
There are two ways to escape, you can choose to use the way back to the tunnel near the stripper or get to the helicopter platform to escape by the helicopter. [NOTE: The escape by helicopter may be bugged in some versions of Contracts. The long route to escape is tedious, but safe. Nobody will bother you.]
This is the longest way to do this mission. You will need the sedative serum for this one if you want to get a Silent Assassin rating. Do not sedate the guard, instead sneak to the police station undetected and retrieve their uniform. Repeat all the tactics from the Assassinating Boris part, but don't kill Boris. Disarm the nuclear bomb, and head back to the second warehouse to put your cop uniform. Now go to the third warehouse via sewer tunnel. The SWAT team will not be suspicious of your presence if you wear a cop disguise so it's really important to do so. Go the upper floor on your right and get into a room with a ladder.
Now, you must wait for the SWAT to attack the ship. Go upstairs and sedate the sniper. Drag his body downstairs and take his uniform and sniper rifle. Boris will then appears on the bridge and threatens to detonate the nuclear bomb, without knowing the fact that his bomb is already disarmed. Snipe Boris out of cold, then hurry back downstairs before the helicopter sees you. Dons your cop uniform and drop the rifle to avoid suspicion. Make your way to the exit to complete the mission.