In the 'pokemon mewtwo origin story', it was a group of scientists who created Mewtwo. They were trying to make a very powerful Pokemon by cloning Mew.
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.
Ash could be one. He has a way of befriending all kinds of Pokémon, and his encounter with a friendly Mewtwo would be an exciting story. He could learn a lot from Mewtwo's psychic powers and wisdom.
However, as time goes by, Ash could come to understand that Mewtwo's overprotectiveness comes from a place of care. He might start to rely on Mewtwo in certain situations, like when they are in an extremely dangerous and unfamiliar territory. Ash could also try to communicate with Mewtwo, asking it to let him handle some things on his own while still appreciating its protection.
The relationship can develop through shared experiences. For example, if they get trapped in a strange dimension together. They'll have to rely on each other to find a way out. This mutual dependence can lead to a stronger bond.