There are a total of 7 Runes available for Corvo to gather in this mission.
#1) In the first main area, there is a path to the right and you can see someone throwing something off of a balcony. Make your way to this balcony, head downstairs and go out the door next to Granny Rags. The Rune will be on the Outsider Shrine at the end of the path right outside the door.
#2) You get a Rune as a reward for doing the first side mission for Granny Rags.
#3) You get another Rune as a reward for doing the second side mission for Granny Rags.
#4) In the area just past the second Wall of Light, there is a trailer building on the left side of the area. The Rune is located inside of this trailer.
#5) Inside the Office of the High Overseer, there is a secret room that can only be opened by pushing a button on a certain statue. When you first arrive at the office, there will be two small rooms off to the sides, that lead to stairs that go to the second floor. At the base of the east set of stairs is a door that leads down to where the statue is. Push the eye to gain access to the secret room, where you'll find the Rune inside of the glass case, which must be broken.
#6) This Rune is located in the Meeting Room in the Office of the High Overseer. It is hanging above the fireplace in the room.
#7) The last Rune for this mission is located in the Back Yard area. It is inside of the Workshop building, on a table. You can enter the building by breaking the glass on the roof, then dropping down inside.
