Leaf would've met Mewtwo in Cerulean Cave and caught him with a Master Ball
From there, Leaf and Mewtwo would've traveled the Pokemon world together, only to return to Cerulean Cave once a year.
Leaf and Mewtwo have a secret base in a house next to Celadon Gym.
Mewtwo has previously been enslaved by Giovanni before he escaped to Cerulean Cave. The remnants of Team Rocket find out about it when a few grunts try to take the Sapphire from Leaf while they were holding Celio hostage. They subjected her to an uncomfortable pat-down when the Master Ball one grunt confiscated sent out Mewtwo, who pushed the few grunts off of Leaf before he coordinated with her to rescue Celio.
Mewtwo worried Team Rocket might target him and Leaf soon, thus they began traveling outside the Kanto region.
Leaf and Mewtwo would have their first romantic kiss when Leaf is 17.
Leaf and Mewtwo start having sex a few days after Leaf's 19th birthday.
Once Leaf and Mewtwo made their relationship official, they founded the Kanto branch of the Pokephiliacs club
Leaf gets pregnant with Haru when she is 25. Though, she named her first child Lumi after she gave birth.