Perhaps in the fanfiction, Mewtwo and Gardevoir are both experimented on by an evil organization. They escape together and have to rely on each other's unique skills. Gardevoir's healing and support abilities combined with Mewtwo's raw power help them survive and seek revenge on those who wronged them. This could involve a lot of action - like battles against the organization's minions and also some emotional moments as they bond over their shared trauma.
One idea could be that Mewtwo, with its powerful psychic abilities, senses Gardevoir's empathetic nature and they form an unlikely alliance to protect a group of weak Pokémon from a common threat. They learn from each other's psychic powers and develop a deep respect for one another.