While Mewtwo hides deep in his cave (we can use Cerulean Cave or a random cave to make up a region as well), he fights off trainer after trainer attempting to capture him. One day, a young woman appears, but she doesn't seek to capture or fight him. Instead, she offers him food and takes a seat to monitor his health, even if he is opposed to it at first.

The second time she arrives, she brings with her items that show she doesn't plan to leave until he knows he is healthy. Due to his distrust in humans, he refuses to telepathically speak to her. He just watches her. In time, he begins to see that she is not only keeping an eye on his health, but chasing away those who want to battle him. To get to him, they have to get past her, which proves to be quite hard. He begins to see the close bond she has with her pokemon and how they trust her.

One day, an earthquake collapses the cave, trapping her inside. When the cave begins to shake a second time, part of the roof collapses over one of her pokemon, and she quickly shoves it out of the way. Realizing she will be crushed, he uses his powers to save her. Although his trust in humanity hasn't changed, he knows she will die for her pokemon and begins to open up to her.

Finally, knowing he is safe and healthy, she decided to leave (with his help to clear the way out). Before she leaves, she questions if he plans to stay in the cave forever, to which he doesn't respond. When she turns to leave, a bit saddened that he would let himself hide away, he asks her that if he were to leave, would she remain beside him. She says he is free to follow her wherever she goes.

So, he does. Although she is happy that he finally joins the world, she quickly sees the danger that is caused when he is seen by trainers and his ever growing protective stance he takes to keep people away from her.

In time, she meets (OC or Canon) who takes an interest in her and the Mewtwo, but Mewtwo is far less than happy when he joins their journey.