Go to The Tree, and walk around it until you see a pathway. Walk underneath the tree, and throw the water toggle here (that you turned on way back in the beginning, with the lever on top of the rails next to the small water tower). This will flood the tree's roots with water in the hole that's dug. Now everything is glowing!
Head back outside and enter the mayor's office again. Go up the elevator one level. Take that path all the way down and go across the dam.
Go left at the fork and up the stone steps, follow the left-most path towards the waterfall. Then go down through the purple portal.
Follow the rocky path until you get to a point overlooking the scrapyard.
Here, you'll see a ramp that can be disengaged, connecting this area to the scrapyard. Push the button attached to that. Then, look behind you and you'll see what looks almost like a helmet with a lever. Throw the lever and push the button. Another seed-swap device! You'll be transported. Where?