How do you open the tower in route 31?
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On emerald there is no route 31 so I am assuming you are talking about route 131. This tower is the one that you get raquaza from. To enter you must go to sootopolis and see kyogre and groudon fighting. Then he will go resolve it. If this doesn't answer your question then reask it with the right route.
If you mean Sky Pillar, you can go two times. The first time, after Wallace disappears from the Cave of Origin, you can find him there and ENCOUNTER Rayquaza. Fly to Sootopolis and you can go straight back. This time, you can catch Rayquaza.
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