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.
Well, it could be about Mewtwo, a powerful psychic Pokémon, and Arceus, the creator Pokémon, having a battle of wits. Maybe Mewtwo challenges Arceus' authority in the Pokémon world, leading to an epic showdown where their powers clash and the very fabric of the Pokémon universe is at stake.
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.
Obviously, the two Mewtwos are the main characters. They are the ones whose encounter drives the story forward.
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.
Arceus is often considered stronger. It's regarded as a sort of god-like Pokémon with immense powers.
A possible main antagonist could be a powerful dark wizard who has somehow learned about the existence of the demigod world and wants to harness the power of the demigods for his own evil plans. He could be jealous of the unique abilities that Percy and Annabeth possess and see them as a threat to his rule in the wizarding world.
It could be the Red Queen. She might see Alice's presence in Mirana's world as a threat to her own power and try to stop their friendship.
It could be a powerful alchemist who has gone rogue and wants to use Naruto's chakra for some dark alchemy purpose.
There could be an ancient force that is awakened by the meeting of Harry and Hela. This force wants to destroy both of them because their combined powers could potentially stop it from achieving its goal of spreading chaos and destruction throughout all the realms. It would use all kinds of devious means to try and separate them and defeat them one by one.
Perhaps an old enemy of Jiraiya who was thought to be defeated but has now resurfaced. This antagonist targets Boruto to get to Jiraiya, thinking that by harming Boruto, he can draw Jiraiya out and finally get his revenge. He would be a powerful and cunning foe, making it difficult for Jiraiya and Boruto to face him.