Ensemble Dark Horse: 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.
Franchise Original Sin: This was one of the first movies to have an antagonist legendary Pokémon who was a Non-Malicious Monster working on its own accord, with the conflict coming from a 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 Starfish Language gives a much better answer to the question of "Why didn't they just explain what they wanted" that is brought up a lot when discussing some of the later movies.
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 Veronica Taylor, 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 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).
This will not be the first or last time Rayquaza would face off◊ against◊ Deoxys.
The green-crystal Deoxys was reduced to a crystal and had to regenerate its body; a very similar concept to the Gems.
Just Here for Godzilla: There is a group of people who only watch this movie because Rayquaza and/or Deoxys is in it.
Magnificent Bastard: "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 regenerating. Years later, Deoxys 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 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.
Nightmare Fuel: 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.
Special Effect Failure: 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.
The Woobie: 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.
