It could be a powerful and jealous Galar trainer. This trainer might see Ash as a threat to their own reputation and success in the region. They would then use their influence and charm to turn Ash's friends against him.
It could be an old rival of Ash who has made their way to Galar and has some sort of vendetta against him. This rival uses the unfamiliar environment and Ash's new relationships in Galar to their advantage, making his friends think he's not trustworthy and causing them to betray him.
Perhaps a new villainous organization in Galar that has its own motives for getting rid of Ash. They might believe that Ash's presence could disrupt their plans for the Galar region, so they manipulate the locals into betraying him.
One possible plotline could be that Ash's new friends in Galar turn on him due to some misunderstanding. Maybe they think he's trying to steal the spotlight in Pokemon battles. For example, if Ash wins a big tournament that some local trainers had high hopes for. Another could be that a villain in Galar manages to manipulate those around Ash into believing he's a threat to the Galar region. This could be by spreading false rumors about his intentions with powerful Pokemon. Or perhaps there's a new type of Pokemon in Galar that has some sort of mind - controlling ability and it's used on Ash's friends to make them betray him.
It could be a jealous rival trainer. This trainer might have always been envious of Ash's popularity and the loyalty of his harem. So, they plot and scheme to turn the harem against Ash by spreading lies and creating discord among them.
It could be a new and powerful trainer who has a vendetta against Ash. This trainer might see Ash as a threat to their own rise to the top in the Pokemon world. They could manipulate Leaf into betraying Ash to further their own goals.
Ash himself could be the main antagonist as he is the one doing the betraying.
Maybe an ancient evil spirit that has a vendetta against Ash. The spirit could possess the aura guardian and make it turn against Ash. In this scenario, the main antagonist is not really the guardian but the spirit that controls it, and the story would be about Ash fighting this spiritual evil.
A new, mysterious organization that is interested in controlling the legendary Pokémon. They see Latias as a key to their plan and Ash as an obstacle to be removed.
A powerful and greedy trainer who wants to capture Manaphy for its rare abilities could be the main antagonist. He might have a whole team of strong Pokemon and use underhanded tactics to try and get Manaphy.
It could be Team Rocket. Since they always cause trouble for Ash in the original series, in this fanfic, they might see Ash's transformation into a Pokémon as an opportunity to capture him and use him for their evil plans.
Team Rocket could always be the main antagonists. They might have a new and more devious plan to steal Ash's Pikachu and other rare Pokemon that Ash and Brock encounter on their journey.
Team Rocket could still be the main antagonists. They might see Ash as a Pikachu and try to capture him more than ever, thinking he's a special Pikachu. Maybe they believe he has some sort of new power because of his transformation.