Hail Sithis!

Walkthrough
First, talk to Nazir and tell him the Night Mother has spoken to you and that the contract is still on. Then you must talk to Amaund Motierre (Who is in the back room of the The Bannered Mare In Whiterun), who will then tell you that the Emperor is on the Katariah ship about to leave Skyrim. He also mentions that Commander Maro will be at the East Empire Company Warehouse docks giving you an optional kill. To get on the Katariah, you have to swim northeast along the river until you see the ship in the middle of the river, then proceed to go underwater and climb up the chain that is holding the anchor, once you're on board there will be several sailors and Penitus Oculatus Agents. (Do not worry if you alert some of the guards on patrol or stationary within the ship as it will not cause the entire ship to be alerted to your presence.)

Continue up the stairs and go south, there will be a ladder to the main deck, to the right of that ladder is the captain's cabin. Captain Avidius drops the Katariah Master Key and various loot. Then go the opposite direction, and go towards the locked door (expert) and use the key you got from Captain Avidius. Upon entering you can see that there is a room to your right with two Penitus Oculatus Agents, with smoke rising from the floor, you may kill them for no negative effects. Continue up the stairs and you will see the Emperor's Quarters, unlock with the master key. You may also get the key by killing the lieutenant who is in the room directly below the Emperor.

Once you proceed inside, Emperor Titus Mede II will start talking to you. He is accepting of his death, stating that this is his and your destiny. He will ask you a favor: kill whoever assigned the contract (Amaund Motierre). He will get up from his chair and proceed to turn his back to you and stare out a window allowing you to kill him backstab him. After you kill him, you can escape the ship through the door to the right. After going through this door, just jump in the water or fast travel away. You then have to go back to Whiterun and enter The Bannered Mare to talk to Amaund Motierre. He tells you the payment is in the dead drop in the cave where you first met. Travel to Volunruud to collect your dead-drop reward of 20,000 septims inside an urn. You must then talk to Nazir in the Dawnstar Sanctuary to finish the quest.

Kill Amaund Motierre (Optional)
If you chose to kill Amaund, who has many valuble gems (which can also be pickpocketed), he will say with his last words "We...had a deal..." as he dies.
 * For those that plan on killing Amaund, immediately after gaining the location of the dead drop, you can hop up on the table, enter sneak, and backstab him with no consequences, or can jump and sit in one of the room corners and when you are hidden you can shoot him in the head with your bow and arrow.
 * He also drops a flawless ruby, which is needed in a quest, this item is Semi-rare, so grab it while you can. (Note: If you are killing Amaund for the flawless ruby, you can also look in one of the rooms in the Emperors Chamber, pass an expert lockpick or use the Emperor's key, look in the end table next to his bed and you will find a flawless ruby.)

Loot
As you enter the Emperor's Room, to the player's left, there is a book on his nightstand. Read it and it will update your map. There are also some valuable gems and necklaces in the room. In front of Emperor Titus Mede II there is a book "Brother of Darkness" which tells some history of The Dark Brotherhood. There is also a map in front of him, the same as the "cloth physical map" that came with the game free of charge, if you pre-ordered. There is also a book called "King" that will raise the two-handed skill. Next to the throne on the Quarterdeck of The Katariah. On the opposite side, on the Forecastle Deck, there is a Scimitar called "Windshear" stuck in the end of the Bowsprit (the long wooden beam protruding from the bow). Windshear has an enchantment where bash attacks using this weapon have a chance to knock down an opponent.

Bugs

 * There is a chance that after assassinating the Emperor you are unable to fast travel or wait. The message: "You cannot fast travel / wait while guards are pursuing you." will appear even though you are in another hold outside Solitude. Using the wait command removes this.
 * There is also a chance that Amaund Motierre will fall through the floor if you kill him while he is sitting in his chair.

Achievements
Hail Sithis