A powerful and ancient Pokémon from a long - forgotten era could be the cause. This Pokémon might have a grudge against Arceus for some past event and has finally found an opportunity to strike and hurt it. For instance, if Arceus had banished this Pokémon in the past, it could now be seeking revenge.
Most likely Arceus is one of the main characters. There could also be other Pokemon or mythical creatures in the story that interact with Arceus in the context of love.
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.
Arceus is a god - like Pokémon, so it seems likely that it would win. But in fanfiction, the rules can be bent. Ash has a lot of experience and a strong will. If he manages to form a powerful alliance with other legendary Pokémon, he might stand a chance against Arceus. However, it's still a long shot as Arceus has near - omnipotent powers.
Maybe a group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
Definitely Pikachu. Pikachu is one of the most recognizable Pokémon, and having it interact with Arceus in a crossover would be really cool. It could be like a small, cute Pikachu following around the all - powerful Arceus.
Perhaps the main antagonist is an entity that represents chaos and destruction itself. It could be a force that is awakened by the meeting of Mewtwo and Arceus, seeing their combined power as a threat to its existence, and thus tries to stop them from achieving whatever goal they have in the fanfiction.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
Obviously, Ash and Arceus are the main characters. Ash is the one being raised, and Arceus is the one doing the raising. But there could also be other Pokémon that are important in Ash's upbringing, like the Pokémon that Arceus assigns to look after Ash or be his companions during his growth.