QR Codes
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If you scanned this QR code the first Pokemon in your box would be cloned.
However, his method only works with the old 1.2 3DS version.
See this video for more information
Powersaves
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Plug the Powersave onto a laptop or computer and insert your cartridge and you can clone as well do another bunch of cool things.
You can buy this from Amazon and eBay. I got mine for roughly around £13.
PKHeX
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Through this method you can inject Pokemon.
Personally its the most complicated method, but you can give it a shot here