Mission 6: Return to the Tower
Just after you climb the water lock and are outside the tower, go to the right where the tallboys are patrolling and enter the small building there. The rune will be just inside on a shelf.
This rune can be found in a chest within the Lord Regent’s personal chambers on the second floor. You will need to enter one of the bedrooms just down the hall from it to find the key on a dresser to enter. Once you have it, go through the large double doors at the end of the corridor and find the regent’s room there.
Rune 6-3 / Outsider Shrine 6-1
When you are in the tower, go to the stairs leading down in the corner to the right of the large stairs in the main foyer. The stairs will take you to the Torturer’s Room in the basement and you will be able to find a rune at the Outsider Shrine in the corner.
Once you reach the Tower Rooftop, you can find this final rune in the planning room. Disable the light wall by taking the stairs on the left side past the library and then enter the Planning Room to get the rune.