PokéBase - Pokémon Q&A
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I know that he used Hyper beam a lot but what else?

That was my fav movie.

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Best answer

Apart from Hyper Beam, it only used one other move, Ice Beam.
Source: http://bulbapedia.bulbagarden.net/wiki/Rayquaza_(M07)

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Hey Nr755,

Aside from the Hyper Beam(s), it was shown once in the Destiny Deoxys movie that it used Sky Drop on the purple Deoxys whilst fighting it. Also, since it is known as the 'Sky High Pokemon', it should have used Extreme Speed as it was traveling around the world looking for the purple Deoxys.