The Hound Pits Pub
Exit the boat and follow the marker to go and speak with Pendleton. If you completed his optional task - Lord Shaw, he will give you a Rune (1/2) as a reward. If not, he’ll give you nothing, but say thanks anyway.
After the chat, follow the marker to chat with Havelock. When you are done, have a chat with Callista in the pub. She’ll tell you she has lost Emily who is hiding from her. To find her, check your room, behind the tower or over near the locked apartment (those are the threes places she appeared for us) and when you locate her, she’ll give you another Rune (2/3) .
When that’s all done with, climb upstairs to Corvo’s bedroom, if you completed the previous mission without killing Lady Boyle, you’ll receive a note and a Rune (3/3) here.
When you are ready, go back downstairs and hit up Piero for any upgrades or ammo restocks required before cruising down to Samuel to start the next assassination mission.