Pokémon has produced over 20 films to date, and while many of the movies' antagonists are sort of forgettable, a few truly stand out among the crowd for their unique characterization and compelling plots. Whether a good villain needs to be threatening or tragic, Pokémon has them all in spades, sometimes presenting truly vile antagonists who see nothing wrong with good ol' fashioned murder, other times, presenting mistreated individuals who need a hug just as much as they need to be stopped.
Looking over the best antagonists in the Pokémon franchise, it becomes clear which villain is top of the pile. Possibly controversially, and despite him being the most beloved Pokémon villain of all time, the best villain isn't Mewtwo.
Solely Threatening Pokémon Villains Are Not Necessarily The Best
Many villains in Pokémon films are just complete monsters. However, it's not enough to just be an overwhelming threat to the heroes in general. You have to put something specific that the main characters value at risk -- threatening one life can be far more effective than threatening the entire world because the stakes are more relatable to the audience. This ensures that the villain poses a direct threat. Some villains, like Lawrence III from Pokémon the Movie: 2000, create environmental hazards that cause more problems than they themselves do directly. That makes them feel small in their own movie.
Some of the most intimidating Pokémon villains include the Iron Masked Marauder from Pokémon 4Ever, Grings Kodai from Pokémon: Zoroark: Master of Illusions and Alva from Pokémon the Movie: Volcanion and the Mechanical Marvel. All of them put their respective movie's main characters at risk in pursuit of their selfish goals, all are willing to kill -- not merely capture -- to get what they want, and almost all of them are the direct cause of everything dangerous that happens to the heroes.
Of the three, the Iron Masked Marauder is simultaneously the most threatening and most basic of them. His objectives are pretty clear-cut from the start: he wants Celebi to rule Team Rocket and the world. To this end, he breaks Misty's leg, tortures an old man, destroys the forest, kidnaps Jessie, and ultimately, is responsible for killing Celebi (though Celebi recovers thanks to time travel). But he's also a fairly flat character.
Grings is another compelling villain -- again, tied to Celebi -- due to his ability to see the future. What makes him interesting is how much of a threat he poses. He can see the future and is an incredibly wealthy businessman. He pretends to be a benefactor to the people of Crown City, but only sees it as a means to maintain his power. He's the closest the Pokémon series has come to introducing a Lex Luthor-type villain. But he's not the best.
A Great Pokémon Villain Needs to Balance Being Sympathetic and Villainous
A high threat level is essential, but what about being sympathetic? Great Pokémon villains need to strike a balance between the two. Villains like Butler from Pokémon: Jirachi -- Wish Maker and Deoxys from Pokémon: Destiny Deoxys are great examples of villains who fail to strike an effective balance between sympathetic and threatening, but still remain memorable in spite of this. Butler is a former Team Magma scientist who wants to power a machine to resurrect the legendary Pokémon Groudon. He is sympathetic because you want to see him succeed, but Butler himself is never as threatening as Groudon.
On the other hand, Deoxys is initially a really interesting antagonist. Deoxys is an alien threat that can regenerate from any attack. For the first half of their movie, this makes the Legendary Pokémon an unstoppable threat. However, once you learn all they're looking for is their companion, they stop being particularly threatening. Again, the balance is not struck.
These villains are simply too sympathetic to be main the scare-factor. Villains like the Iron Masked Marauder and Kodai are better fitting for this requirement; however, there are two villains who fit it almost perfectly. Though, in the end, one comes out on top.
Why Mewtwo Is Close but Isn't the Best Pokémon Villain
In terms of villains who strike a balance between sympathetic and threatening in the Pokémon franchise, Mewtwo from Pokémon the Movie: Mewtwo Strikes Back and Molly Hale from Pokémon 3: Spell of the Unown are the best examples. Mewtwo is obviously the fan-favorite villain, even receiving a sequel special, Mewtwo's Revenge, as well as a remake of his original movie (the Mewtwo in Pokémon: Genesect and the Legend Awakens is a different Mewtwo). However, Molly Hale just works better as a villain.
Mewtwo is a deeply tragic character. The extended prologue of the original Japanese film he features in reveals his experiences with Ambertwo and establishes the cloned Pocket Monster as profoundly unfortunate, but the version most English-speaking audiences saw in theaters remains sad even with this part cut. In essence, he's a creature created as a weapon but seeks a new purpose. This purpose ultimately turns Mewtwo against the world and he uses his power to try to destroy all original life and replace it with clones.
Mewtwo hits all the sweet spots a good villain needs to. He's a threat to both the world and the Pokémon trainers individually that he encounters -- kidnapping all their Pokémon, cloning them, and then nearly killing Ash. That makes him a huge threat on a personal and global level. However, Mewtwo stops being sympathetic after his prologue, instead, transitioning into an incredibly intense villain whose motivations you understand but whose actions you can't condone in any way. On top of that, Mewtwo never directly engages any of the heroes in combat for a prolonged amount of time -- the human ones, at least. He's too absurdly powerful to really do that himself. This means that for most of the film, the characters just stare in awe of Mewtwo, which results in a lot of scenes of quiet tension but not as satisfying a payoff as there could have been.
Why Molly Hale is the Best Pokémon Villain
By contrast, Molly Hale never stops being sympathetic. Unlike Mewtwo, she's just a girl who has lost her entire family and, unbeknownst to her, this tragedy results in a group of Unown channeling her imagination through their reality-warping abilities. She creates a super-powerful version of Entei that, by design, cannot be defeated. She even kidnaps Ash's mom, which makes the stakes very real to the franchise's human face. She goes onto beat every one of Ash's friends, one by one, and even his Charizard, in one of the most epic fights in the series.
There is something so intimidating about a childlike imagination gone out of control, especially when Molly's wishes manifest in such grotesque ways. But at the core of it all is just a scared girl who desperately needs love. It's genuinely heartbreaking watching her process her loneliness over the course of the movie.
Sure, you might understand Mewtwo's motives, but with Molly, you actively want her to find happiness. Her villainous methods are toxic to her, trapping her in a dream world that's keeping her from finding real happiness. That's the true tragedy of her character, and it means by beating her, the heroes actually help her. In the end, Molly Hale is the best Pokémon movie villain for being so much more than just another world-destroying monster.