Well, it could be that Latias has been influenced by an ancient prophecy. According to this prophecy, Ash is the key to unlocking a great power. But she can't just ask Ash to come with her as she fears he will be stopped by his friends or other Pokémon trainers. So, she decides to kidnap him. As time passes, Ash manages to communicate with Latias and understand her motives. He then decides to cooperate with her, not because he has to, but because he realizes the importance of the situation.
Ash would probably be very confused at first. He might try to reason with Latias, asking her why she is doing this. If she doesn't respond, he would start looking for ways to escape. He would also be worried about his Pokémon and his friends, wondering if they are safe.
In this fanfiction, it might be that Latias controls Ash as part of an experiment. Latias is a curious Pokémon and wants to see how a human like Ash would react in different scenarios. So she uses her powers to make Ash explore areas he might not have otherwise, like a hidden and mysterious part of the Pokémon world. This could lead to Ash discovering new Pokémon species or even new types of Poké Balls. As he's being controlled, his initial fear turns into a sense of adventure as he experiences things he never thought possible.
In this kind of fanfiction, perhaps Gary has some extreme jealousy towards Ash. Maybe he kidnaps Ash because he wants to prove himself superior in the Pokémon world. He could be tired of always being in Ash's shadow and thinks this is a way to get the upper hand.
One possible plot could be that there is some sort of a prophecy in the Pokémon world that foretells the birth of a special baby from a human and a legendary Pokémon like Latias. Ash gets involved in this prophecy without knowing at first. As the relationship between Ash and Latias develops, they find out about the baby. The baby could have a great destiny, like being the bridge between different Pokémon species and humans. Ash would have to teach the baby about the values he believes in, like friendship and perseverance.
A plot could start with Latias being in some kind of danger, and Ash comes to her rescue. This leads to them spending more time together. As they get to know each other better, they realize their feelings are more than just friendship. After getting married, they might have to deal with people or Pokemon who don't approve of their relationship at first. But through their kindness and the strength of their love, they win them over and continue their happy life together.
Well, it could be about Ash somehow magically being transformed into a Latias. Maybe he then has to deal with the powers and instincts that come with being a Latias. He might try to find a way to turn back while also exploring the world from a new perspective as a Pokemon.
Perhaps in this fanfiction, Ash goes to the town in search of a rare Pokemon item. But when he arrives, he discovers that Latias and Latios are in trouble because of some evil forces. So, Ash decides to help them out. He uses his battle skills and knowledge of Pokemon to fight against these forces. Along the way, he also learns about the unique culture and traditions of the town.
Ash could catch Latias in a place full of ancient ruins. Latias might be guarding some sort of Pokemon relic there. Ash shows respect for the place and Latias' role. This makes Latias interested in him. Eventually, Ash catches Latias and they go on to discover more about the relic's power together.
A possible scenario for their betrayal in fanfiction is that a powerful organization kidnaps someone Ash loves and forces Latias to betray him as a ransom. Latias, with no other choice, has to do what the organization says. Ash would then be left feeling betrayed, not knowing the real reason behind Latias' actions at first. This could lead to a story full of mystery, action, and ultimately, redemption.
Well, it could be that Latias uses her psychic abilities to influence Ash's decisions in the story. Maybe she manipulates him into going on a particular adventure or making a choice that he wouldn't have otherwise made.