Get to the diplomatic vessel
This stage can be completed in two ways. You're on a ship. The default way is to hijack the ship. In order to do so, you have to get to the captain's quarter, kill him and take the helm. If you don't want to kill, check out the alternative...
After returning to gameplay on the ship, quickly get to the nearest room. On the desk there, which a guard approaches sometimes, you'll find a document. If you can manage to counterfeit it quickly, by holding the interact button (you have to hide underneath the table and wait until the guard moves away), you won't have to hijack the ship. However, you can't be exposed! After counterfeiting the document, you have to wait a second - a man will come and take the document to the pilot.
Next step will take you to the ship's bow, on a lower floor, where a small ballista is - shoot it and you will create a pathway to the vessel. The other ship is much larger and has many rooms.
The main vessel and the issue of finding the scepter
There are two quests to complete on the ambassador's ship (the second will only become active if you get close to one of the three people-targets). The second quest, optional, is about stealing 3 insignia from the soldiers. They are on the upper decks, one on each of the joined ships. It's enough to follow them quietly and steal from behind, or kill them and loot the insignia. Just don't push them off the ship - you will never retrieve the artifacts. The guards are highlighted so spotting them is easy as a pie.
Getting back to the main objective: you have to get to the stern of the second ship (the middle one). After reaching the ship, walk down the slipway and jump - try to grab the woodwork of the window and then make your way left - towards the crane. Climbing onto it, get to the 3rd floor through the window. Open the door to the room (one unarmed man inside) and take the stairs to the 4th floor.
This level is joined to the middle ship - go there. The gap at the stern is small enough for you to jump to the second level. To get to the first level, where the target is, you have to go through a cabin. You can jump down at the center, behind the handrail of the stairs that lead down.
Time to double back. After the cut-scene, you'll find yourself outside and the alarm to be triggered. Climb on the nearest rope and go to the next vessel. Enter the cabin via the nearest door and exit through the other door. The following path should keep you away from enemies.
Repeat the same trick - from the window's woodwork, try to leap onto the balcony. Enter the room and turn right, then exit through a small window on the stern. From there you can get higher. You will get to the highest floor via stairs.
The only thing left to you is making your way to the ship's bow, where the saving balcony is located. Don't worry about guards (just don't trigger any alarms). When you approach the balcony and untie the rope, a cut-scene will commence, during which no one can harm you.