Maybe there's a fanfiction where an evil organization is after Latios and Latias, and Ash has to protect them. He teams up with his Pokemon and uses their combined skills to outwit the bad guys. Ash could use Pikachu's speed and electricity, along with the flying abilities of his other Pokemon to create distractions while he gets Latios and Latias to safety.
One idea could be that Ash forms a special bond with Latios and Latias while on a journey in a new region. They help him discover a hidden power within himself. For example, Latios might be able to sense when Ash is about to make a wrong move in a battle and communicate it to him telepathically.
Through shared adventures. For instance, if they get lost in a mysterious forest together. Ash would rely on Latios or Latias's ability to sense their surroundings and they would grow closer as they face the challenges of finding their way out. It could be as simple as Ash sharing his food with them during this time, showing kindness.
One idea could be that Ash and Latias team up to save a group of Pokémon from an evil organization. Ash uses his battle skills and Latias uses her psychic powers.
There could be a fanfiction that focuses on the bond between latias and latios. Maybe one of them gets injured and the other has to go on a journey to find a special healing item. Along this journey, they learn more about themselves and their relationship, and also about the wider pokemon world.
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.
Another theme is protection. Latios and Latias are powerful Pokémon, and in fanfictions, they might protect Ash from various threats, whether it's other powerful Pokémon or some evil organizations. And sometimes, Ash also tries to protect them in return. For example, in some stories, an evil team might be after Latios and Latias for their powers, and Ash steps up to defend them. There can also be themes of exploration, where they all travel to new and mysterious places in the Pokémon world together, discovering new Pokémon species and secrets along the way.
A good plot. It should have an interesting story that involves Ash, Latias, and Latios in a meaningful way. Maybe it could be about their adventures together, or a special bond that forms between them.
A plot could involve Rayquaza and Latias finding a strange, powerful artifact that has the potential to either save or destroy their world. They have to figure out what to do with it. Rayquaza might want to destroy it right away, fearing its power, while Latias believes they should study it further. This creates conflict between them, but also a chance for character growth as they try to make the right decision.
One possible plot twist could be that Latios and Latias are actually under the control of a more powerful and evil Pokémon. Ash initially thinks he's caught them to protect them, but then discovers he has to fight against the real threat that has been manipulating them all along.
Well, a good plot could be that Latios gets injured and Latias has to go on a quest to find a special healing item for him. Along the way, she meets other Pokémon who either help or hinder her. Or, they could be caught in the middle of a battle between two different Pokémon factions and have to use their unique abilities to bring peace. Also, a plot where they explore a new, uncharted region together and encounter strange new Pokémon and phenomena.
I really like 'Latias and Latios: A New Beginning'. In this fanfiction, they encounter a new type of Pokemon that has never been seen before. It shows how they adapt to this new situation and how their relationship evolves as they try to figure out what this new Pokemon is all about. It's full of mystery and adventure, which makes it a great read for any Pokemon fan.