Maybe there's an evil organization in the fanfiction. They could be after a particular Pokemon that Ash and Nora have or know about. Their goal is to use this Pokemon for their own malicious purposes, like taking over the Pokemon world. This organization would send out their minions to constantly attack and try to capture Ash and Nora's Pokemon.
One possible main antagonist could be a powerful and arrogant trainer who wants to prove that he is better than Ash and Nora. He might try to steal their Pokemon or sabotage their battles.
Perhaps a group of bandits who steal Pokemon and sell them on the black market. They see Ash and Serena as threats because they are trying to stop their illegal activities. These bandits could be led by a really tough and mean - looking guy who has no mercy when it comes to getting what he wants. They would constantly be trying to sabotage Ash and Serena's attempts to protect the Pokemon and the people in the medieval setting.
Often, Team Rocket can still be a main antagonist. They might come up with new and devious plans to steal Ash's Pikachu or Serena's Pokemon. Their comical yet persistent attempts to cause trouble add a lot of action and humor to the fanfiction.
Perhaps a powerful and mysterious trainer. This trainer is jealous of Ash's connection with his Pokemon and his ability to conduct these experiments. He wants to prove that he is the better trainer. So he tries to disrupt Ash's experiments by challenging him to battles at inconvenient times. He also spreads false rumors about Ash's experiments being dangerous to other Pokemon, which causes some local Pokemon communities to be hostile towards Ash.
It could be Team Rocket. They are always causing trouble for Ash and his Pokemon in the Pokemon series, so it's likely they would be the antagonists in this fanfiction too.
There could be a new group of villains. Maybe they are a secret organization that has been watching Ash for a long time. They fear that his secret could disrupt their plans for world domination in the Pokemon world. So, they constantly try to stop him from uncovering his own secret.
A group of rogue scientists who are experimenting on Pokemon in unethical ways could be new antagonists. They might be creating powerful and dangerous hybrid Pokemon.
There could be a rogue legendary Pokemon that sees Ash's transformation as a threat to the natural order. This legendary Pokemon, with its own set of motives, could be trying to prevent Ash from becoming a fully - fledged legendary - like being. It might set up various obstacles and battles for Ash, testing his will and strength at every turn.
One type of antagonist could be a corrupt Pokemon League official. In the fanfic, this official might bribe Ash to do something unethical, like throwing a battle against Iris. When Iris finds out, she'll feel betrayed. Another likely antagonist is a Pokemon hunter. If the hunter captures a Pokemon that Ash and Iris both care about, and Ash, in an attempt to rescue it, makes a deal with the hunter that seems to go against Iris's values, she'll feel betrayed. And sometimes, it could be a self - centered Pokemon trainer who wants to be the only star. They might set up Ash and Iris to fight each other and make it look like one has betrayed the other.
One interesting plot could be Ash and Nora teaming up to discover a new and rare Pokemon species. They might face challenges like difficult terrains and other trainers trying to stop them.
Team Rocket could be the main antagonists. They're always causing trouble for Ash and his friends, and they'd surely be after Ash and Leaf on their journey too, trying to steal their Pokémon.