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I have defeated the evil tree tret and it says its to wesak to undo what it has done turn people into trees and not sure what to do next.
Use the healing water on the tree. The glass bottle you filled up at the mercury lighthouse. :) GS is one ofthe best RPG's I have had the pleasure to play... roll on the second installment :)
Go to Gamefaqs.com and they've got a partially made walkthrough which can tell you the story of Golden Sun 2: The Lost Age!