Here's every battle theme used by nonlegendary special Pokémon (i.e. Mythical, Ultra Beast, and Paradox Pokémon) from the core series Pokémon games!
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Timestamps:

00:00: Mew (Emerald)
01:26: Deoxys (FireRed/LeafGreen & Emerald)
04:10: Deoxys (Omega Ruby / Alpha Sapphire)
06:53: Arceus (Diamond/Pearl/Platinum)
09:17: Arceus (Brilliant Diamond / Shining Pearl)
11:41: Arceus (Legends: Arceus) [All Phases]
15:44: Ultra Beast (Sun / Moon / Ultra Sun / Ultra Moon)
18:32: Paradox Pokémon (Scarlet/Violet Area Zero Wild Battle)
22:25: Paradox Pokémon (Scarlet/Violet Area Zero Ambush Battle)

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Silvuddy's Notes:

Mew: Much like Kanto's Legendary Pokémon, Mew simply received a remix (making 4 total versions in Generation 3!) of the Kanto Wild Pokémon theme (though in Emerald, this makes sense since the theme appears nowhere else in Hoenn). The only way to hear this theme on a GBA was with the Japanexclusive event item "Old Sea Map" to take a trip to Faraway Island and find Mew.

Deoxys: Deoxys is the first mythical Pokémon to receive a unique battle theme, as well as the first to be challenged in battle without the use of an event (thanks to its story inclusion in ORAS). The theme is incredibly alien with chimes, glitchy blips, and pitch bending synths, and the triplet bounce of the whole thing make it quite intense as well.

Arceus: This DPPt version of this theme is impossible to hear legitimately in battle, and only can be heard in the HGSS Arceus event cutscene (not a battle), due to the Azure Flute item necessary to encounter Arceus never being released officially. Legends: Arceus still paid homage to those who knew about the secret, technically unused battle theme by remixing it for the true final boss battle against Arceus. With complete save data from L:A, BDSP would also enable a fight with Arceus, which included its own arrangement of the original music, to finally challenge the Pokémon god in the Hall of Origin like we always hoped.

Ultra Beast: This is a super wacky battle theme that is weird and awesome in all the best ways. Sitar and phasing synths are a combo I never knew I needed; this tops Deoxys for mostalien sounding battle theme IMO!

Paradox Pokémon: Technically they don't have a unique theme, as the Area Zero Wild Pokémon theme plays for every Pokémon encountered in the crater, not just Paradoxes. However, a percussionheavy remix of the theme does play when a number of Paradox Pokémon ambush the player and their friends before entering the Zero Lab.

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(All music obtained from https://downloads.khinsider.com/, Mixeli, Bliitzit, and NintendoMelody. Please check them all out!)

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