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.
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 plotline could be that Ash is betrayed by his so - called friends in the Pokémon world. They might spread false rumors about him, making everyone turn against him. Meanwhile, Mewtwo, who has formed an unlikely bond with Ash, is also betrayed by the scientists who created it again. They try to recapture Mewtwo to use it for their evil experiments. Ash and Mewtwo then team up to fight against their betrayers and prove their worth.
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.
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.
One possible reason could be jealousy. Maybe his friends are jealous of Ash's success in his Pokemon journey. For example, if Ash wins a big tournament and gets all the fame, his friends might feel left out and betrayed. Another reason could be a misunderstanding. Ash might do something that his friends misinterpret. Say he makes a deal with an enemy in order to save his Pokemon, but his friends don't understand the situation and think he's turned on them.
Perhaps in this new region, Ash discovers a powerful new Pokemon that others want to control. His friends, fearing the power of this Pokemon, betray him to protect the region. They might think that Ash is being too reckless with this new discovery and that it could lead to destruction. It could also be that there's a prophecy in the new region that Ash is somehow involved in, and his friends misinterpret it and believe he's the cause of potential harm.
Perhaps Ash has been deceived by a false prophecy or a mysterious figure. This false information could lead him to believe that capturing Arceus is the only way to save the Pokémon world from an impending doom. So, in his misguided attempt, he betrays Arceus.
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.