A really cool plot could be that Mewtwo and Ash get transported to a parallel dimension where the rules of the Pokémon world are different. They have to figure out how to get back while also dealing with new and strange Pokémon and challenges along the way. This would test their relationship and their ability to adapt in a completely new environment.
In some fanfiction, there might be a plot where Mewtwo, after being initially hostile towards Ash, gradually comes to respect him. This could involve Ash showing Mewtwo the true nature of friendship and trust through his actions with Pokémon.
Well, one possible interesting plot could be Ash using his unique bond with his Pokémon to outwit Mewtwo. Maybe he convinces Mewtwo that not all humans are bad through the kindness shown by his Pokémon team.
One interesting storyline could be Ash befriending Mewtwo in a more in - depth way. Maybe Mewtwo decides to travel with Ash and his team, and they face challenges together. Ash could help Mewtwo understand the true meaning of friendship and trust, which Mewtwo has always struggled with due to its creation and past experiences.
One interesting storyline could be Ash and the female Mewtwo forming an unlikely friendship. They could start off as strangers, with Mewtwo being cautious of Ash due to her past experiences with humans. But as Ash shows kindness and understanding, they gradually grow closer. For example, Ash could help Mewtwo when she is injured in a battle against a powerful enemy. Another could be a story where they team up to save the Pokémon world from a new, mysterious threat that neither of them could face alone.
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 interesting aspect is the exploration of their unique bond. Ash's kind-hearted nature could be shown to gradually break through Mewtwo's guarded and often aloof exterior. For example, in some stories, Ash might help Mewtwo understand the true meaning of friendship and trust.
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.
Often, a key plot point is Mewtwo's struggle to fit into the world of regular Pokémon and trainers, while traveling with Ash. Since Mewtwo is a genetically created Pokémon, it has a different view of the Pokémon world compared to others. Another plot point could be the battles they face together. Mewtwo's power combined with Ash's battle strategies make for some epic encounters.
One possible motive could be that Mewtwo sees Ash as a threat to its own power or freedom. Ash is constantly on a journey to catch and train Pokémon, and Mewtwo, being a powerful and intelligent Pokémon, might view Ash's actions as a potential danger to its kind or its own existence.
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.