One possible plot could be that Mewtwo discovers a hidden place where the Unown reside. The Unown, with their mysterious powers, initially seem like a threat to Mewtwo. But as the story unfolds, Mewtwo realizes that they are more complex. Maybe the Unown are trying to protect a powerful secret or an ancient artifact. And Mewtwo has to decide whether to help them or take the power for itself.
In the fanfiction, Mewtwo could be on a quest to understand its own origins further. During this journey, it stumbles upon the Unown. The Unown, being able to create illusions and warp reality, show Mewtwo different versions of its past. Mewtwo has to decipher which one is true while also dealing with the Unown's unpredictable behavior.
The plot might involve a trainer who has a special connection to both Mewtwo and the Unown. This trainer gets caught in the middle of a conflict between Mewtwo's desire for power and the Unown's need to maintain the balance in the Pokemon world. The Unown could start causing strange events to keep Mewtwo at bay, and the trainer has to find a way to make peace between the two.
Mewtwo might initially be hostile towards the Unown. It's a powerful and often solitary Pokemon, and the Unown's strange abilities could be seen as a threat. So it could try to attack or control them.
It could also be that Mewtwo is misinterpreting the intentions of humans. In the fanfiction, it sees a large - scale Pokemon capture operation as a threat to all Pokemon. So it decides to take matters into its own hands and starts 'hurting' those involved in the operation, which includes both trainers and their Pokemon. But eventually, through communication and understanding, things are resolved.
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.
Maybe she gets separated from the other Mewtwos at a young age and is raised by a kind trainer. This trainer helps her to develop her powers in a different way compared to the other Mewtwos. Along the way, she has to face off against other powerful Pokemon who are jealous of her unique abilities and her relationship with her human trainer. As she grows, she becomes a symbol of hope for other female Pokemon who are often overlooked in battles and competitions.
In a'mewtwo meets mewtwo fanfiction', it could start with the two Mewtwos being summoned by an unknown force. At first, they are confused and defensive. As they interact, they find out that their memories of creation and the pain of being experimented on are very similar. They might then decide to search for the source of this unknown force together. Along the way, they face various challenges, like other powerful Pokémon trying to stop them or humans who fear their combined power. But through their shared experiences and newfound bond, they are able to overcome these obstacles.
Perhaps a new trainer who has a unique ability to communicate with Pokemon on a deeper level. This trainer, despite being new, has an innocent and pure heart. They see Mewtwo not as a monster but as a Pokemon in pain. So they step up to try and soothe Mewtwo's rage using their special gift.
The plot could be about Mewtwo trying to control Missingno's glitch powers.
In this kind of fanfiction, one possible scenario is that Ash forms a special bond with Mew. Mew, being the mythical and playful Pokemon, could lead Ash on an adventure full of surprises. Maybe it shows Ash some hidden powers within Pokemon that he never knew before. This could help him in his battles and his journey to become a Pokemon master.
One possible plot could be that Ash gets exposed to some strange energy during an adventure. This energy starts to transform him gradually into Mewtwo. As he changes, he begins to experience Mewtwo's memories and powers. He might struggle with this new identity, trying to figure out how to control the immense psychic abilities. Meanwhile, his friends are both shocked and worried, not sure how to deal with this new Ash - Mewtwo hybrid.
In this fanfic, perhaps there is a prophecy that only Mewtwo and Lugia together can fulfill. The prophecy might be related to saving the Pokemon world from a great disaster, like an approaching asteroid or a dark force that is spreading across the land and sea. They start as strangers, but as they begin to understand the prophecy and their roles in it, they form a deep bond. Mewtwo uses its intelligence and combat skills, and Lugia uses its natural strength and connection to the elements to face the impending doom.