Moment Subpages are Spoilers Off. You Have Been Warned.
- The visuals of the Pokémon and their attacks are stunning, especially Gengar's Double Team and Pikachu's Volt Tackle.
- At the start of the movie, Cubone causes a small explosion when it hurls its bone club at Tim. It drives home the common message in the games that even small, unevolved Pokémon can be dangerous to humans if one doesn't have any Pokémon of their own for protection.
- Tim getting Mr. Mime to give up information by successfully miming his own method of interrogation.
- Tim jumping into the arena to protect Pikachu from the corrupted Charizard.
- Magikarp's evolution into Gyarados. Not only is it the first time Pokémon evolution is shown on-screen in the film, but type advantage or no, it's not every Pokémon that can make a Charizard cower in fear.
- Psyduck finally letting loose with one of its headaches, blowing away the Greninja (who are supposed to No-Sell it even then by virtue of also being Dark-types) pursuing the heroes and shaking a huge patch of forest.
- Howard manages to recapture Mewtwo, take over its mind with a neural transmitter, and use its powers to forcibly fuse humans with their Pokémon all across the city.
- This movie really shows off how dangerous Ditto's abilities can be (at least when it's a genetically enhanced/modified Ditto), for purposes of espionage and trickery as well as its versatility in combat. Tim was only able to neutralize Ditto by exposing it to R, making it lose control of its powers. And even that was only possible because it was pretty clear that Ditto was toying with him instead of changing immediately into an overwhelming form that would have ended the fight instantly.
- Roger breaking out of his restraints and smacking away Ditto, who is about to throw Tim off a skyscraper. In doing so, he saves a kid he barely knows.
- When Pikachu returns to the city and sees all hell breaking loose, his immediate reaction is to try and put a stop to it by challenging Howard-as-Mewtwo. His attacks are repeatedly overpowered, but he keeps trying, finally getting a solid hit in by Volt Tackling Howard into a building. Howard recovers soon after and gloats that Pikachu has no hope of beating him, but Pikachu reveals that his efforts had simply been a distraction, allowing Tim to sever Howard's link with Mewtwo.
- Worth noting is the music that kicks in as Pikachu decides to take Mewtwo on. The 8-bit chiptunes at the start make it clear the production crew know the source material, they know the audience wants some classic Pokémon action, and they're about to deliver.
- Bill Nighy as Mewtwo. Granted, it's Howard controlling Mewtwo, but the fact that the actor, known for playing hammy and terrifying villains, manages to make Mewtwo even more intimidating and outstanding than they already are.
- Lucy immediately realizes the danger of Chemical R at the parade, runs down the street, yelling at the bystanders to prevent the Pokémon from inhaling it. While it doesn't accomplish much, it's still very brave, especially since she's putting herself in danger of getting blasted.
- Mewtwo proper doesn't see much action in this movie when it's not under Howard's control, but the World-Healing Wave that it produces to undo all the damage Howard wrought still gives a hint of its immense power.
- The movie could have easily strongly marketed Generation I Pokémon to appeal to the mainstream media like it (and most other media that also have a history on banking on nostalgia like Transformers and Power Rangers) has often done, but instead, the marketing and the movie itself pays respect to all of the then-current seven Generations. Sure, Generation I still gets the Pyroar's share, but each of the seven Generations has at least one visibly marketed and highlighted representative, each given time in the limelight.
- Initially, Generation IV somewhat seems to get the short end of the stick by only having one representative active, namely the many gigantic Torterra, and the only other three featured members of that Generation—Dialga, Palkia, and Arceus—are relegated to statues. However, the latter three are used well, in the form of creating symbolism and foreshadowing Howard's attempts to play God.
