PokéBase - Pokémon Q&A
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So.... I invited an Ace Trainer to my base in the Secret Isle and changed or slogan to "SPARTA!!!" and went to battle him in an Inverse Battle (my format.) Battle stars, cool music all the norm the he send out a SHINY GENESECT... KO'ed it though the he sent out Darkaria KO'ed that the he sent out a shiny Rayquazza. At this point my jaw was at the floor and used Flare Blitz for a quick super-effective KO to asses what had just happened. I thought I caught Rayquazza, can someone give me a hint on how rare this was if rare at all?

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This is actually quite common. Secret Base teams are generally based (hahaha) on the team you have in your party in-game. This Ace Trainer happened to have a Shiny Genesect, a Darkrai, and a Shiny Rayquaza on his team when you recruited him. Thus, he had these Pokemon when you battled him.

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