During the game's ending, you will ride a final elevator (the "Wonkavator").
You aren't supposed to solve this one until after you have completed the game.
After you ride the Wonkavator, and everything you've done becomes undone, you'll start with a fresh perspective on things.
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After seeing this gate lit up again, you'll probably realize that it can form an environmental puzzle when aligned with the sun.
This also has other consequences, which is why it is comes at the very end of the game. (Or, technically, right after the end of the game).
At any point after activating this puzzle, you can simply reload your save file and turn the gate off. You'll be free to keep exploring the island and the symbol will remain lit on the obelisk.
Bonus Note:
It is actually possible to turn the gate back on without restarting the game (although no one initially discovers it this way). If you bypass the Wonkavator ending and instead do... other things, you'll find a piece of paper. You can then come back to the starting area and use the info on that paper to turn the gate back on again, without restarting.
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Solution (contains MAJOR SPOILERS):
If you haven't done so yet, just beat the game and you'll understand where to find this one.
Roll over each black area below for hints.
Each new hint gives away more than the previous one.
Map
Town Obelisk
SW #8
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Intro
This might be considered the most monumental environmental puzzle in the game.
We strongly encourage you to find this one on your own. At a certain point in the game (and not when you might expect), the game gives you a huge clue about how to solve it.
This puzzle is folded in with the game's story in a way that if you keep playing, you will probably discover it in the "intended" way, at a very appropriate time.
When you were first near it, you didn't know about environmental puzzles.
When you returned to its area, it was no longer in a solvable state.
It is located in the starting area.
The results of solving this puzzle are rather paramount, so the rest of the hints are full of spoilers.
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So, here's the twist:
Keep your eyes open as you ride the Wonkavator. While most things are disappearing, this one puzzle will appear.
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At the beginning of the game, there was a large electrical gate you had to turn off to leave the starting area.
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Location:
Hints:
If the electrical gate is off, this puzzle is impossible to solve.
When you ride the Wonkavator, the gate turns back on (just before dumping you to a new game).
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Perhaps in this new game, you'll notice how the gate, when closed, produces a bright white light.
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The final key is the sun.
Roll over each black area below for hints.
Each new hint gives away more than the previous one.
If you have actually completed the game, and you are now hunting for environmental puzzles, then you might have missed the "intended moment."
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Although there are a few ways you could (theoretically) find this one, almost all players find it a certain way -- which seems to be the intended method -- so these hints will describe that "intended method."
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Pre-Spoiler Info:
THE WITNESS - ENVIRONMENTAL PUZZLE HINT GUIDE