* AssPull: The 'Poké Ball Management System' has never been mentioned before or after this movie. According to the movie, Poké Balls need a wireless signal in order to function and for a trainer to call out their Pokémon. Not only does this [[FridgeLogic bring up questions WHY it would need a wireless signal in order to function]], it [[FridgeHorror brings up the horrific implications of Pokémon potentially being forever trapped in a Poké Ball]]. Even later on in the anime proper when Ash winds up in Ultra Space, his Poké Balls function without any problems, making it clear the writers only came up with it for this movie for the sake of increasing tension.
%%* CreepyAwesome: Deoxys.
* EnsembleDarkhorse: Rebecca due to being a {{Meganekko}} with both Metagross and Tyranitar (seen in a later movie), making her one of the few anime characters with more than one pseudo-legendary, especially notable as both pseudo-legendaries are also popular Darkhorses themselves.
* FranchiseOriginalSin: This was one of the first movies to have an antagonist legendary Pokémon who was a [[spoiler:NonMaliciousMonster working on its own accord, with the conflict coming from a [[NotEvilJustMisunderstood misunderstanding]] rather than the purple-crystal Deoxys actually being evil]]. While relatively new for the films at the time, many have accused later movies of doing that exact pair of tropes over and over again to the point of annoyance. It doesn't help that Deoxys being an alien with StarfishLanguage gives a much better answer to the question of [[spoiler:"Why didn't they just explain what they wanted"]] that is brought up a lot when discussing some of the later movies.
* HarsherInHindsight:
** Ash's last line in the English dub of the movie ("Hey Pikachu, I'm glad that you and I will always have each other.") becomes this to fans of the 4Kids dub after the entire English cast, including Ash's own voice actor, fan-favorite Creator/VeronicaTaylor, was replaced by new voice actors in 2006, the year after this movie was released in the U.S.
** It also serves as vague but clever {{Foreshadowing}} of [[Anime/PokemonLucarioAndTheMysteryOfMew the next movie]], where that very line would be tested (and where the 4Kids voice actors would be playing their roles for the last time in a Pokémon movie).
* HilariousInHindsight:
** This will not be the first or last time Rayquaza would face [[http://archives.bulbagarden.net/media/upload/e/e3/RayquazaDeoxysLEGENDUndaunted89.jpg off]] [[http://archives.bulbagarden.net/media/upload/e/ee/ORAS_Mega_Rayquaza_Deoxys_artwork.png against]] [[VideoGame/PokemonRubyandSapphire Deoxys]].
** [[spoiler:The green-crystal Deoxys]] was reduced to a crystal and had to regenerate its body; a very similar concept to [[WesternAnimation/StevenUniverse the Gems]].
* JustHereForGodzilla: There is a group of people who only watch this movie because Rayquaza and/or Deoxys is in it.
* MagnificentBastard: [[NonMaliciousMonster "Purple" Deoxys]] arrives on Earth to search for its "Green" counterpart, willing to go to any lengths to reunite with its partner. Quickly reacting to the presence of Rayquaza, Deoyxs cleverly uses its various {{shapeshifting}} forms to fight off its foe, facing even total disintegration by slipping away and slowly [[FromASingleCell regenerating]]. Years later, Deoxys [[AlienInvasion invades [=LaRousse=] City]], shorting out its technology and using an army of clones of itself to kidnap most of the populace, making its search for its still-missing partner easier. Anticipating the arrival of Rayquaza, Deoxys finally locates its Green counterpart, and [[EnemyMine chooses to work with Rayquaza]] in saving Ash and his friends from [=LaRousse=]'s rogue robot army, Deoxys earning Rayquaza's respect before departing Earth for good.
* NightmareFuel: The opening provides two strong examples:
** First, when Deoxys' meteor first impacts, Tory is knocked down onto the shelf below and nearly trampled to death by panicking Sealeos and Walreins.
** Followed soon thereafter by the Deoxys/Rayquaza fight. One of the first Legendary Pokémon battles to have innocents literally caught in the middle, trapped between flailing bodies and deadly energy blasts by two extremely powerful combatants that either do not know you're there, or do not care. Made worse by the fact that it's taking place in an arctic environment, and some of that collateral damage is happening to equipment you may need to survive even if you do make it through the actual battle.
** The CGI Deoxys are surprisingly genuinely unsettling, with their empty husk like appearance and pitch black eye holes.
* SpecialEffectFailure: Plenty of the CG has not aged well, and it's especially obvious with the two main legendaries. There's a reason why there's less CG in later ''Pokémon'' movies.
* TheWoobie: You kinda have to pity Tory for having a phobia of Pokémon in a world where they are everywhere and a near constant part of life.
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