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.
Perhaps in the fanfic, a new and mysterious Pokémon arrives. This Pokémon is able to manipulate the thoughts of those around it. It makes Mewtwo believe that Ash is a threat to all Pokémon. So Mewtwo starts to act against Ash. Ash, on the other hand, is clueless as to why Mewtwo has suddenly turned on him. He has to dig deep into the secrets of this new Pokémon and find a way to reverse what it has done to Mewtwo.
A possible plot could be that Mewtwo, in an attempt to protect Ash from a powerful and mysterious enemy, undergoes a self - imposed TF. This transformation gives Mewtwo the ability to access a hidden power within itself. Ash, on the other hand, has to figure out how to communicate with this new - formed Mewtwo and together they face the common foe. Throughout the story, their relationship evolves as they learn more about each other's capabilities.
A possible plot is that Ash, while in Mewtwo's form, is hunted by those who fear Mewtwo's power. He has to use his own knowledge of friendship and teamwork, which is so characteristic of Ash, to convince the people and Pokemon around him that he's not a threat. This could lead to some really cool battles where Ash, in Mewtwo's body, shows his unique fighting style combined with Mewtwo's strength.
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.
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.
One idea could be that Ash uses his unique battle style which he has developed over his journey to create a really challenging gym. He might include Pokémon from all the regions he has visited in his gym battles, making it a diverse and exciting experience for trainers. For example, he could have Pikachu lead the charge as always, but also include some of his less common Pokémon like Heracross or Gliscor.
One idea could be that Mewtwo and Ash are forced to team up to save the Pokemon world from a new, powerful and evil threat. They start off distrusting each other due to their differences, but as they face challenges together, they begin to understand and respect one another.
A possible plot is that Ash is on a journey to a mysterious place that is said to be Mewtwo's lair. Along the way, he meets various Pokémon and trainers who have either had encounters with Mewtwo or know something about it. When he finally reaches Mewtwo, Ash doesn't try to capture it forcefully. Instead, he shows Mewtwo the beauty of the Pokémon world and the relationships between different Pokémon and trainers. This makes Mewtwo intrigued and willing to be captured by Ash.
One idea could be that Ash discovers a female Mewtwo in a hidden part of a forest. She's initially scared of humans but Ash manages to communicate with her using his bond with Pokemon. They go on a journey together to find a place where she can live in peace, away from those who might want to use her powers.
One idea could be that Ash discovers a wounded Mewtwo and nurses it back to health. As they spend time together, they form an unbreakable bond that challenges the way both Pokemon and humans interact. Another plot could involve Mewtwo using its powers to help Ash reach a new level of Pokemon training. For example, it could allow Ash to experience telepathic communication with his Pokemon, enhancing their battle strategies.