Well, it's possible that Ash and Mewtwo team up in the fanfic. They could face a common enemy together. Mewtwo's incredible psychic powers combined with Ash's experience and determination would make them a formidable duo. And perhaps this encounter would change Ash's view on some things, like the true nature of Pokémon battles.
It could be that Mewtwo is on a quest to find its true origin or purpose. Ash joins Mewtwo on this journey. Along the way, they meet other powerful Pokémon and trainers. There are battles and competitions, but also moments of self - discovery for both Ash and Mewtwo. The fanfic might explore themes of identity, friendship, and the power of Pokémon in a more profound way through this plot.
Perhaps in the fanfic, Ash has achieved a lot in his Pokémon journey, and Misty has also become a more skilled Pokémon trainer. When they meet again, they start to compare their experiences. Ash could show Misty his new and powerful Pokémon, and Misty could introduce Ash to some new training techniques she has learned. And then they decide to train together for a while to improve their skills even more.
In an 'Ash into Mewtwo' fanfic, one aspect could be the change in relationships. His Pokémon might not recognize him at first, and he'd have to find a way to communicate and regain their trust. Also, trainers like Misty and Brock would be shocked. The fanfic could delve into how Ash tries to convince them that he's still the same person inside, just in a different form.
It could be a new, powerful and evil Pokemon trainer. This trainer has a dark past and wants to use Mewtwo's power for his own selfish and destructive purposes. He might try to capture Mewtwo by any means necessary, seeing it as the ultimate weapon to dominate the Pokemon world.
Well, one way is through shared dreams. Mewtwo could enter Ash's dreams and they could communicate on a deeper level there. This would be a very unique way to develop their relationship as it's not a typical form of interaction. Ash could learn more about Mewtwo's fears and hopes in these dream encounters.
The relationship could start with mutual respect. Ash respects Mewtwo's power and intelligence, and Mewtwo respects Ash's courage. Then, through shared experiences like helping other Pokémon in need, they start to trust each other more. This trust can then turn into a deeper emotional connection.
Maybe a mysterious organization that is trying to capture all the Pokémon in the area where Ash and Misty meet again. They would be the antagonists as Ash and Misty would try to stop them. This organization might have some powerful Pokémon and devious plans that Ash and Misty have to figure out and defeat.
A possible plot for an 'Ash into Mewtwo' fanfic is that the transformation is a result of a wish granted by a magical Pokémon. Ash, now in Mewtwo's body, decides to use this opportunity to understand Mewtwo better. He travels to the places Mewtwo has been, meets the Pokémon Mewtwo has interacted with, and tries to solve the mysteries surrounding Mewtwo's creation. Along the way, he also has to face the consequences of having such a powerful form, like being hunted by Team Rocket who want to use him for their evil plans.
One idea could be that Ash and Mewtwo form an unexpected bond. Mewtwo, being so powerful, could initially be distrustful of Ash. But Ash's pure heart and determination slowly break through Mewtwo's defenses. They might go on a journey together to stop a new evil threat that is targeting Pokemon with strong psychic powers. Another plot could involve Mewtwo using its powers to help Ash understand some of the mysteries of the Pokemon world that he has been curious about for a long time.