Instructions
Travel to Sneyato Forest. When you reach the forest, a cutscene shows Marco running away from Thomas and declaring that he does not need Thomas's help. To reach Thomas again, you need to solve the sphere puzzle in the woods.
Walk north and west until you reach the red sphere. Touch the red sphere. The red barriers blocking Yushima and a treasure chest open. Walk directly south of the red sphere to reach the treasure chest.
Return to where Yushima is standing and go through the red barrier. Touch the second red sphere. The red barrier closes.
Touch the purple sphere directly across from the red sphere.
Exit the red barrier behind Yushima and walk right to the first red sphere you touched. Touch it again.
Walk south past the treasure chest you opened originally until you reach a fork in the road. Walk right to reach the save point. Save your game and cross the purple barrier to reach Thomas.