there was a gamefaqs thread about this, so i thought id share it
1. Save in front of the PC in the Battle Tower.
2. Deposit the pokemon you want to clone in an empty box.
3. Leave the PC and save again.
4. Go to the PC one more time and withdraw the pokemon you want to clone, the one that's in an empty box.
5. Talk to the lady on the far right, and she will ask you to join a Multi Battle.
6. Select Yes and choose any two pokemon.
7. When she asks if you want to save, select Yes.
8. If everything so far has been done correctly, the game will wait about one second before doing anything else.
9. It doesnt matter what you do from her, the One Second wait was the glitch taking place.
10. Turn off your game, and now the cloned pokemon is both in the PC and in your party.
btw this is 100% verified to work, and is a cool way to get more tms or hold items or even master balls if you want. with the advent of d/p, assuming item trading works, this is going to be rather helpful.
however nobody knows the long term effects, so it might create corrupted data after awhile, i dunno
edit: also anyone with shinies or pokemon with sweet ivs should clone them and trade them over wifi imo :[[[
wow theres a huge thread on cloning!! i love this place :)
i havent read all 5 million pages, but thought i'd throw my two cents in, just to say that the process can be simplified somewhat. (note that my post might just be old news, so sorry if it is.)
namely, if the pokemon you want to clone is already in the computer, you dont need to withdraw it so you can begin by depositing it. so here is a simplified version of the process.
1. make sure the pokemon(s) you want to clone are in the PC and that you have enough space in your party so you can withdraw them. (and make sure that when you withdraw them, you will have two pokes eligible for the battle tower - eg at least 2 non-ubers both with different items).
2. save your game. (anywhere is fine, but you might as well be in front of the said PC.)
3. now proceed from step 4 of the above.
this quicker method is particularly good if youre doing mass clonings.
also you can clone items without needing to clone pokemon. brilliant if you want 1000's of rare candies.
1. start by having at least two pokes in your party that are eligible for the battle tower. give an item to any pokemon in your PC.
2. save game as usual.
3. go to the PC, select move items, and put the item you want to clone in your bag.
4. go through the steps about going in the battle etc.
5. when you turn the game on, the poke in your PC will have the item, and it will also be in your bag.
note that you can do many items at once this way. in theory you could do as many items as pokes on your PC. i can clone a hundred rare candies in a few short minutes now that i have a few boxes full of pokes holding rare candies.
i thought i had an idea to REALLY speed it up, but it doesnt work. i thought you could deposit items from your bag to the PC item storage instead of step 3 above. that way you can put 99 rare candies in the PC in a couple of seconds. but alas it didnt work (it also didnt do anything bad, like delete things).
if this is old news, sorry...... if it helps, good :)