Team Rocket is an obvious choice. They could use some new, devious hypnosis device to control Ash for their own gain, like trying to steal all his Pokémon.
It could also be a powerful Pokémon with hypnotic abilities that has its own motives. For example, it might hypnotize Ash to stop him from interfering with its plans to take over a certain area or disrupt the balance of nature in some way.
A new, mysterious Pokémon trainer who is jealous of Ash's success could be the antagonist. This trainer might hypnotize Ash to make him lose battles and damage his reputation.
It could be Team Rocket as always. Since Ash is now a Pikachu, they might see it as an easy target to capture. They could have new gadgets specifically designed to catch Pikachu - Ash, and constantly try to get their hands on him throughout the fanfiction.
Another possibility is that the main antagonist is an evil scientist who was responsible for Ash's transformation in the first place. This scientist could be trying to create some sort of chaos in the Pokémon world by turning a well - known trainer like Ash into a girl. And now, Ash as a girl has to stop this scientist from causing more harm to the Pokémon world.
It could be a trainer who has a starter that has a type advantage over Ash's new starter. For example, if Ash has a Squirtle and the antagonist has an electric - type starter like Pikachu, they would constantly be in conflict. The antagonist might be jealous of Ash's skills or the potential of his Squirtle and try to undermine him at every turn.
A powerful psychic alien that has been lurking in the shadows could be the antagonist. This alien has been observing Ben for a while and decides to use hypnosis to make Ben do its bidding. The alien's motives could be related to some intergalactic power struggle, and by controlling Ben, it hopes to gain an advantage over its rivals.
It could be a new character, like a powerful wizard who has a grudge against Percy for some reason. Maybe Percy accidentally disrupted one of his spells, and the wizard is out to get him, which makes Percy mad.
It could be a lone wolf type of character. This person is a survivor in the same world as Clementine but has gone a bit crazy from all the hardships. They see Clementine as a competitor for resources and decides to shoot her to get rid of the competition.
It might be an accident - causing character. This could be someone who is clumsy or irresponsible. Their actions, even if not intentional, end up causing harm to Judy. For example, they might accidentally start a fire in a place where Judy is, and she gets burned in the process.
It could be Draco Malfoy. In some fanfictions, Draco might be pushed to such an extreme by his family's beliefs that he resorts to physical violence against Hermione. He might punch her out of jealousy or to assert his so - called superiority.
Dr. Eggman could be the antagonist. He's always trying to defeat Sonic, and shooting him could be part of one of his evil plans. Maybe he developed a new weapon specifically designed to take Sonic down.
It could be an unknown villain who has a special ability to hypnotize. This villain might be targeting Ichigo because of his power.