Your destination now is the tower which used to be occupied by Emily. As you can probably remember, the room on one of the top floors of the tower, can be reached through the footbridge shown in the above screenshot, which you can reach starting from Corvo’s chambers (on the third floor of the pub building), and by walking over the workshop’s roof.
Approach the door and interact with it. This will result in initiating a conversation with Callista, who has been hiding here.
New Main Quest: Use the flare launcher in Emily's tower to signal Samuel
After the conversation ends, search around the room for Emily. You will find an Emily's tower key), a Letter to Callista, a Sokolov’s health elixir and Piero’s spiritual remedy. Finally, interact with the flare launcher shown in the above screenshot.