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I didn't know what to do once I went to the Blissey Secret Base, so I made the Blissey owner my Secret Pal. Will he have a Blissey when I battle him?

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If you challenge him in his Secret Base:

Yes, he will have Blissey.

If you challenge him as a Secret Pal in your Secret Base:

No, he will have the NPC Pokémon.


Source: Experience

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What a fast answer! Impressive!
It's kind of funny, because when I challenged him in my Secret Base, he had three Blisseys.
Odd… all of my Secret Pals have NPC Pokémon.
All of my secret pals have their own Pokémon, i know because they have really rare Pokémon and legends, shinies, plus random levels, like lv73 or something.
I swear I registered a Blissey Base as a friend, and all they had were NPCs… but there's a good chance I'm mixing it up with the people in the Blissey Base.

Time to put Mario Kart DS aside for a second and pull out the ol' Omega Ruby.