The Pokémon Mystery Dungeon series revolves around the player character becoming an actual Pokémon. They form a rescue team with other Pokémon to help those in need by escorting Pokémon to their friends, rescuing some of those friends, and even potentially ending the apocalypse while they're at it. They can also recruit other Pokémon encountered in the dungeons as close allies as well.
However, there are some Pokémon that act as antagonists towards the protagonist and their rescue team. These antagonists might have their own rescue team, deceive the protagonist and friends, and even try causing the apocalypse that the protagonist ends up fighting against.
10 Scraggy Tries Scamming The Protagonist's Party
Scraggy first appears in Gates To Infinity as a scammer helping Gurdurr to steal gems from the protagonist after they initially retrieve them from the dungeon as an exchange for Gurdurr building their home. However, Scraggy eventually turns a new leaf after their exploits are discovered, and eventually starts working at the Move Shop with Quagsquire as a much better Pokémon while Gurdurr stops his scamming ways.
9 Beheeyem Literally Petrifies Pokémon
Pokémon Super Mystery Dungeon introduces Beheeyem as not just one of the antagonists in general, but also the antagonist that specifically gave the player their amnesia in the game. They initially attack the protagonist as a force of many and are incredibly hostile towards them.
However, one of the Beheeyem ends up revealing that they were being controlled by the true antagonist of the game, the Dark Matter, and broke away from the rest of the pack to warn the protagonist and the others. However, the fact, that Beheeyem also ended up literally petrifying other Pokémon doesn't help its cause.
8 Drowzee's Thievery Served As An Early-Game Boss
Drowzee appeared in Explorers of Sky/Time/Darkness as one of the early antagonists. He kidnaps Azurill to get the treasure found in Mt. Bristle. He's a tough boss to beat early in the game in battle. This is because he is capable of using Confusion to hit the party hard, as well as put them to sleep with Hypnosis. In turn, he's completely immune to sleep-inducing moves and Sleep Seeds with his Insomnia, and Forewarn helps him block the party's attacks occasionally. However, he quickly abandons his criminal ways after the protagonist and their team beat him, and he even helps Azurill with his nightmares as a way to atone for his previous actions.
7 Nuzleaf Manipulates The Protagonist But Was Also Being Manipulated Himself
In Pokémon Super Mystery Dungeon, Nuzleaf initially takes on a guardian role for the protagonist. This quickly turns into a heartbreaking moment where he manipulates the player to activate the Luminous Spring so he could destroy it himself. However, it turns out that Nuzleaf is being possessed by the true antagonist of the game, the Dark Matter. Additionally, Nuzleaf is so repentant of his actions that he leaves Serene Village after he regains his senses, out of guilt and shame for what he did. However, he does return to help the protagonist defeat the final boss in the end, along with Beheeyem and Yveltal.
6 Yveltal Was Brainwashed By Negativity
Yveltal, in Pokémon Super Mystery Dungeon, serves as one of the main antagonists. Even though it was also brainwashed like Nuzleaf and Beheeyem by the Dark Matter, this Dark-type Pokémon petrified the player, the player's main partner, Archen, Suicune, and Raikou at one point, which was a brutal moment for Pokémon fans. Additionally, this aggressive Pokémon has hard-hitting attacks like Oblivion Wing that make it difficult to defeat in battle.
Its ability, Dark Aura, makes its Dark-type allies more powerful as well, making the battle against Yveltal even more difficult. Though Yveltal doesn't appear until late in Super Mystery Dungeon out of all the antagonists, he's still a tough one to beat.
5 Gengar Was A Definite Meanie To The Protagonist's Party
In the Red And Blue Rescue Team games, Gengar first appeared as the leader of Team Meanies, an evil team. He later accused the protagonist of being the Pokémon cursed by Ninetales after letting his Pokémon take the bullet for Ninetales' attack when provoked. This cursed human-turned-Pokémon would apparently bring disaster. This resulted in the protagonist and their partner being forced to temporarily flee the village as refugees. However, it was later revealed that Gengar himself was the former human-turned-Pokémon.
4 Dusknoir's Deceit Made Him An Effective Plot-Twist Villain
Initially, when Dusknoir is introduced in Explorers of Sky/Time/Darkness, he's well-known as an amazingly skilled explorer, and this quickly makes him a local hero in the village. However, it's later revealed that this Ghost-type Pokémon came from the future and a doomed one that he wants to maintain for his own sake. What makes him a villain is that he manipulates the protagonist and his partner into helping apprehend Grovyle, who was also from the future. The plot twist surprise of Dusknoir as a villain surprised fans of the games, and he still holds up as an effective villain to this day.
3 Munna Runs A Group Aimed On Destroying The World
The adorable Munna is one of the main antagonists in Pokémon Mystery Dungeon: Gates To Infinity. Munna initially presents herself as a sweet, innocent Pokémon who was a victim of Hydregion's ambush, but it turns out that she's part of a group of Pokémon allied with the main villain, the Bittercold, to destroy the world. She goes as far as claiming that destroying the world is the best way to end all suffering.
Many fans were horrified to discover Munna of all Pokémon as a villain, but her deceptive innocence until the reveal makes her one of the most effective villains in the entire series.
2 Darkrai Wants To Make The World A Perpetual Nightmare
Darkrai wants to turn the world into a literal nightmare and does this by stealing the Time Gears in the Explorers of Sky/Darkness/Time games. He tries to manipulate the player and their friends into ending their own lives and rule the world through neverending darkness and nightmares. He traps other innocent Pokémon in nightmares to achieve this goal, making Darkrai seem like he's meant to be in a horror movie.
In the end, even with the protagonist and the party slowing down his plans, it takes Palkia's intervention to completely end his plans. He ends up becoming amnesiac after this, and the protagonist can even recruit him after finding him wandering the dungeons.
1 Kyurem Foretells The End Of The World And Almost Succeeds With It Happening
Kyurem, the Dragon/Ice Pokémon that can see the future in Gates To Infinity, acts as the main antagonist before it's revealed that the Bittercold is the true antagonist. Kyurem, much like Dusknoir from Explorers Of Time/Darkness/Sky, wants to protect the world's future. The bad news is that said future is a doomed one, and so Kyurem comes to blows with the protagonist and their party over it. Kyurem is so insistent on keeping the world's doomed fate as is that he is willing to keep fighting the protagonist over it to the bitter end, even if he doesn't actually want that to happen himself. Even though Bittercold is the true antagonist at the end, Kyurem is a villain that is relentless in achieving his goal.