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After you beat the Delta Episode, and go back to the Mossdeep Space Center, 2 scientists on the second floor ask about Deoxys saying the following,

"If you learn anything new about Deoxys, please let us know at your earliest convenience."
"What reason could Deoxys have to seek out of the Hoenn region? We will continue to investigate that topic."

I tried bringing Deoxys to them, but nothing happened. Was what they said supposed to trigger anything?

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did you bring it in a a different form?

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He says this because, if you fainted Deoxys, he would tell you where it is, but if you caught Deoxys, the scientist doesn't matter at all.

Source: I fainted Deoxys and he told me.

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I wish i knew that before i soft-reseted 6 times from before I caught Rayquaza just because i kept K.Oing Deoxys. XD Thanks~
No Proplem. When I fainted Deoxys I was like, There goes my chance of catching Deoxys, the he said that Deoxys was at Sky Pillar, and I was like, YES!