Meta Battle Subway PokeBase - Pokemon Q&A
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The first one you can find is at the back of the rock-filled section on Route 10.

If you have a Pokémon with maximum EVs, you will be able to access Super Training, and if you complete Follow Those Fleeing Goals! you will receive an additional Thunderstone.

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You can go to the Stone Emporium in Lumiose city.At first there will only be the fire,water and leaf stones which cost 1200 poke dollars.After progressing in the game come back to the emporium and the Thunderstone will be there.

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Adam's answer is correct, but you can also find it through super training as one of the secret training prizes.

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