Continue up the stairways until you get to the moving platform.
Climb on board. This will bring you to the top platform of the big machine we activated earlier, just about the strange Russian box. Go to your left to release the ladder so we don't have to worry about getting back here again.
Stay up top, and keep on this path. Take the elevator down, find the seed-swap device, and activate it.
You'll appear in what was once the stone sphere, but this time, it's been replaced with wood. Head down and around, and push the button below to spin the globe so that the stairs going up (the higher staircase) are pointing directly towards the building set into the cliffside (The Tower/ Mayor's office) with the steel beams hanging out.
Re-enter the wood sphere/platform and use the seed-swap device.
Now the stairs going down should be in front of an entrance to another area.
There'll be a bunch of beetles flying around. Head to the bottom, and read the papers inside on the table/desk. Remember the number. Write it down (It changes in every game). Remember the complicated Russian machine with all the lights and so many buttons? If you enter this number in, you'll get an achievement (Sweet Revenge) on Steam.
Now go back up and go back to Hunrath with the seed-swap device. Rotate the sphere so that the upwards stairs are facing the door with the metal board lock in Kaptar. The staircase going down should be facing the Tower.
When you goes into the Tree, You should stop the machine.
Now that you're back, go to the door. Throw the metal board lock up, and move through the doorway. Head straight across the shrine and back to where the Polyarch skeleton is. Continue along this path, and pass through the portal at the bottom again. Follow this path all the way to the end, going up the stairs all the way until the stairway leading down that you ignored before. Go down that staircase. At the bottom, there's a small cutout with another seed-swap device inside. Activate it.