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This achievement can be earned during Mission 7, A Crack in the Slab.

After obtaining the Timepiece from The Outsider, leave the room via time travel, similar to how you would for the "Under the Table" achievement, and remain in the past (with the manor fully restored). Take the first door on your right in the hallway and you will find yourself in a kitchen. Time travel to the present, loot the cabinet directly in front of you for a key, then return to the past. Move towards the back of the kitchen and down the small corridor. Use the key to open the locked door, time travel to the present, turn left, and hop out of the broken window (beware of the hound in this courtyard).

Pass through the sealed doors on the left-hand side of the courtyard and you will emerge into a large, debris-filled chamber. Hug the left wall and make your way downstairs into the basement. Time travel back to the past and you will notice two guards in the room ahead. Take both of them out however you'd like, grab the red crank wheel in the display case to the left of where they were, and then throw that wheel into the hole in the wall (the same hole one of the guards was looking through).

You can now switch back to the present, jump through the hole, grab the wheel and attached it to the pipe on the left-hand side of the flooded room, and crank it to drain the water. Once the room has been drained, turn around and you will find a Rune atop a wooden crate. The achievement will unlock after picking up the Rune.