You can battle the Pokemon again. Just beat the elite four and it will be there. If you don't want this problem just get a action replay and get all items so you can have 995x master balls.
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you cant unfourtanately
Empoleon is not a legendary Pokemon. It is the final evolution of Piplup, one of the starter Pokemon in Pokemon Diamond, Pearl, and Platinum.
capture the legendary and train your Pokemon
when you get your seventh badge and you will head for mount cornet
you can go after the legendary pokemon, or beat him again.