It could be that Arceus betrays Ash by revealing that all of Ash's Pokemon encounters and relationships were fabricated. Arceus made it so that Ash would form bonds with certain Pokemon to further its own ends. For instance, Arceus wanted to study the power of friendship among humans and Pokemon through Ash's experiences. When Ash finds out, he feels used and betrayed. He might then set out on a journey to free his Pokemon from Arceus' control and restore their true free will.
There might be some new characters introduced in the fanfiction. A mysterious Pokemon trainer who has some ancient knowledge about Arceus and can guide Ash. Or perhaps a group of Pokemon researchers who have been studying the relationship between Arceus and the world for a long time. These characters could add more depth to the story, providing different perspectives on the situation between Ash and Arceus, and helping Ash in his fight against the perceived betrayal.
Well, it could be that Ash makes a discovery that goes against Arceus' grand plan and is thus betrayed. Maybe he finds out something about the balance of the Pokemon world that Arceus doesn't want known.
One possible plot could be that Ash discovers Anabel has betrayed him by siding with a rival trainer in a crucial tournament. This could lead to a rift in their friendship and Ash having to find a way to overcome this setback and prove himself without her support.
One possible plot could be that Ash is falsely accused of a serious crime within the Pokémon world, and Greninja, due to some misinformation or outside influence, turns against him. Maybe a powerful villain manipulates Greninja's mind, making it believe that Ash is a threat to the Pokémon world. This could lead to intense battles between them, with Ash being heartbroken and trying to prove his innocence while also trying to save Greninja from the villain's control.
Perhaps Ash is wrongly accused of something in Skyla's hometown. Skyla believes the false accusations and turns her back on Ash, which makes Ash feel extremely betrayed. He then has to prove his innocence not only to Skyla but also to the whole town.
Perhaps a new and powerful trainer arrives in the story. This trainer manages to deceive Ash's harem members, making them think that Ash is a hindrance to their growth as trainers. As a result, they side with the new trainer and betray Ash, leaving him feeling confused and alone.
In some fanfictions, Arceus might be bound by some ancient rules that Ash unknowingly breaks. These rules are so important to Arceus that it feels compelled to betray Ash. For example, if there's a rule about not interfering with a certain type of Pokémon evolution and Ash does it accidentally, Arceus could see it as a major transgression and take action against him.
One possible plotline could be that Ash is raised by Arceus to be a sort of Pokémon messiah. He is taught the true essence of Pokémon and is sent on a quest to save the Pokémon world from an impending doom.
Another plot could be that Arceus is in some sort of trouble and Ash is the only one who can save it by capturing it. This could involve a complex story where Ash has to figure out what's wrong with Arceus and how to use his skills to capture it in a way that helps it.
Ash would likely be extremely heartbroken. He has always had a deep connection with Pokemon and believing that Arceus, a powerful and supposedly benevolent being, has betrayed him would be a huge blow. He might become withdrawn at first, not knowing who to trust anymore.