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How do I use Poke Transporter?

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I opened the app and it said, "Do you want to transfer this box" and showed me this box that I didn't want to transfer. I said no and went to my game. I couldn't find that box anywhere! Which box does Poke Transporter use to transfer Pokemon???

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PokeTransfer transfers ALL Pokemon in Box 1.

Click here for a guide. (Although he's not really guiding us, he's still showing you what do. So it's great manipulation :P)

Hope I helped. :)
Source: Above Link

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Thanks!
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this is a step by step, if that is needed by anybody:

A)put all Pokemon(up to 30) you want to transfer into "box one" on the BW/B2W2 game card and SAVE the game. use home button to get back to home menu.

B)select Pokemon transfer from home menu. allow the application to transfer the entire box of Pokemon as it was designed to do, make sure it said it was saved on Pokemon transfer and game card. use home button to return to home menu, shut down Pokemon transfer and shut off system.

C) remove the BW/B2W2 game card and insert X or Y game card. turn on system. once at home menu, select Pokemon bank, and allow application to boot up. if you did not turn off system to switch games, hoping to simply go strait onto Pokemon bank, you will not be able to access Pokemon bank, and will be kicked out at this point.

D)select use Pokemon bank from game menu, and you will be directed to the box one of the first 'group' in the the Pokemon bank(note that this is customizable, this is explained for default set up). the transfered Pokemon can be viewed in and shuffled from as desired from the transfer box, to get to this box, simply press the 'L'(left) trigger/corner button while the arrow is on the box area of the upper screen.

E)Important: for future use of Pokemon transporter, all transfered Pokemon must be removed from the transfer box, either into a bank box or a box on X or Y game card, it does not matter, the box just has to be emptied. this has to be done every single time transporter is used, and this is the part I find very annoying... sooo... tedious......>:c

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