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.
Maybe an ancient and powerful Pokemon that has been awakened from a long slumber. This Pokemon is filled with rage and wants to destroy everything in its path. It sees Mewtwo as a threat and Ash as a nuisance. It uses its unique and terrifying powers to try and eliminate them both. For example, it could have the power to control the minds of other Pokemon and make them turn against Ash and Mewtwo.
Perhaps the main antagonist is an entity that represents chaos and destruction itself. It could be a force that is awakened by the meeting of Mewtwo and Arceus, seeing their combined power as a threat to its existence, and thus tries to stop them from achieving whatever goal they have in the fanfiction.
Obviously, the two Mewtwos are the main characters. They are the ones whose encounter drives the story forward.
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.
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.
It could be a jealous rival trainer who mocks Ash for wearing a dress and tries to use it as a way to undermine his confidence and stop him from competing in Pokemon battles.
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.
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.
It could be a powerful warlock who has found a way to manipulate time and space. He wants to stop Paige and Prue from joining forces because he fears their combined power. So he creates various obstacles and illusions to keep them apart.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
A powerful new pirate group could be the main antagonist. They might be after the same treasure or territory as Luffy and Shanks. They could have some unique and dangerous abilities, like the ability to control sea monsters. Their leader could be a former crewmate of a well - known and feared pirate, who has his own vendetta against both Luffy and Shanks for some past reasons.