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This mission introduces a new mechanic to Dishonored 2, and this makes the collectibles harder to get. It's a mind-bending mechanic, but we'll get through this together.
Table of contents
Walkthrough
Rune 1
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Before things get weird, you can grab the first rune without any drama. Head up the stairs you see as soon as you come through the doors. Head into the room ahead of you and head to the left.
Rune 2
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From here on, things get complicated. Starting in the cellar, head to the past. In a corner to the right of the elevator, you'll find a crank wheel in a case. To the right of there, you'll find some boxes stacked like stairs that lead to a hole in the wall and a nearby note warning of a leak. Pick up the crank wheel and throw it through the hole.
Travel to the present where you'll find a flooded basement. Swim down to pick up the crank wheel and then to the left where you can attach it to a drain valve. Drain the cellar, and you'll find a rune nearby.
Bonecharm 1
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Head back to the elevator. Climb up onto the barrels stacked in front of the elevator doors and jump toward the top of the elevator. There's a small ledge you'll land on. Travel to the past and open the hatch to climb on top of the elevator. Travel back to the present and drop into the elevator to find your first bonecharm.
Bonecharm 2
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On the first floor, toward the front of the building, your heart will tell you about a bonecharm that you can never quite get to. Look for a weird garbage fort. Travel to the past and climb under the desk. Travel back to the present to gain entrance to the room and then travel back to the past before the bloodflies notice you.
There's a dead dog and a note on the floor warning about bloodflies. Burn the dog's body in the furnace in the past to prevent the bloodflies in the present. Now that they're out of the way, travel back to the present to find the combination to the safe (this is random, so our numbers probably won't work for you). Head back to the past and enter the combination to find a black bonecharm.
Painting 1: The Commutative Rats and the Weeper and Blueprint 1: Firing Chamber Pivot
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Also on the first floor, near the dining room, there's a large vault that's inaccessible in the past. Travel to the present to get inside and then back to the past again. Here, you will find your first painting and the level's only blueprint in the safe.
Bonecharm 3
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Head to the balconies overlooking the dining room in the past. All the way to the right, there are three levers on the wall. Switch them all to the up position to raise all three chandeliers as high as they will go. Hop across to the far chandelier and then come back to the present. Turn around and climb up the falling rafter to find another bonecharm.
Rune 3
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The next rune and painting are also on the second floor. Head to the main atrium and up the dust slope (in the present) or stairs (in the past). Take a right at the top and work your way back along the hall.
In the present, watch on the left for a note about replacing a damaged window. Travel to the past and discourage the workers nearby from completing their job either with unconsciousness or murder. When you come back to the present, the window will be missing.
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Hop onto the iron rafter and then through the window on your right. You'll enter a photo studio. Take out the guards in the past and grab the rune you find to the left.
Painting 2: The Torturer's Quaternionic Groan
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In the present, go back to the iron rafter. Follow it the rest of the way around and jump to the balcony. Back in the past, take a right to find the other painting in a nearby room.
Bonecharm 4
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After you learn what you're here to learn and handle Stilton however you see fit, check his office for another bonecharm.
Bonecharm 5
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On your way back through the transformed Dust District, there are a few more things to grab. As you exit the mansion, keep to the left. Head inside the office you see there, and work your way through a few more closed doors to find a bonecharm.
Rune 4
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Back outside and a bit further down the path, Far Reach up to the wooden walkway on the right to grab another rune.
Bonecharm 6
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Just past there, Far Reach your way up to a familiar rooftop to grab another bonecharm.
Bonecharm 7

Almost back to the skiff, where the Pastor was on your first time through, you'll pass one more bonecharm. Keep your heart out, and it's hard to miss.