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Is it to do with Deoxys being extra-terestrial or something like that?

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I assume you are talking about the movie.

It is because that is how they communicate. Throughout the whole movie, one Deoxys is searching for the other and calls out to him via Aurora. Though he may communicate like this because he is extraterrestial, it just does not appear out of nowhere like Kyogre and Rain.

Source: I watched the movie.

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that was an epic movie