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Even though the Battle Tower is for battling, it is also a place of Pokémon Restrictions and unfortunately several Pokémon cannot enter the Battle Tower...here is a list of the ones you cannot use:

No. Poké-pic Pokémon Name
#198 Kyogre
#199 Groudon
#200 Rayquaza
#201 Jirachi
#202 Deoxys
#305 Mewtwo
#306 Mew
#384 Lugia
#385 Ho-oh
#386 Celebi