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 possible scenario in this fanfiction could be that Ash encounters Mewtwo in a new, uncharted region. Mewtwo, being intrigued by Ash's unwavering spirit, decides to test him. Ash passes the tests with the help of his Pikachu and other Pokemon. This leads to Mewtwo seeing Ash as a worthy trainer and allowing itself to be caught. It would be a great twist on the usual Pokemon-catching storylines.
Themes can vary widely. However, the concept of trust is often explored. How does Ash gain Mewtwo's trust? It could be through his actions in battles, his respect for Pokémon, or his ability to see Mewtwo not just as a powerful entity but as a being with feelings. Additionally, the theme of the underdog (Ash) facing the seemingly unbeatable (Mewtwo) is quite prevalent. It makes for an exciting narrative as we see Ash use his wits and heart to achieve the seemingly impossible task of catching Mewtwo.
The plot could involve Ash hearing rumors about Mewtwo's location. He sets out on a journey to find it. Once he does, he tries to communicate with Mewtwo. Mewtwo initially resists but Ash's pure intentions start to sway it.
Perhaps Mew and Mewtwo are in a fight against an evil force that threatens the Pokémon world. Ash arrives at the scene and manages to communicate with them. He offers his help and through their combined efforts, they defeat the evil. As a result, Mew and Mewtwo see Ash as a true hero and allow him to catch them, leading to a new chapter in Ash's Pokémon journey.
There's a fanfic where Ash catches Mew and Mewtwo during a special tournament. The story focuses on how Ash has to face off against powerful trainers who also have their eyes on Mew and Mewtwo. It's a great read as it shows Ash's growth as a trainer and how he strategizes to keep these two Pokémon safe from those who might misuse their power.
There are quite a few on fanfiction websites. Some focus on how Ash's kindness and determination lead to him catching Mewtwo. For example, in a certain fanfic, Ash manages to catch Mewtwo during a battle where he shows Mewtwo that there is more to life than power. He shows Mewtwo the beauty of friendship among Pokémon and humans, which ultimately makes Mewtwo willing to be caught by Ash.
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.
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.