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 idea could be that Rayquaza and Latias team up to protect a special place in the Pokémon world. Maybe there's a dark force threatening a beautiful and magical forest that is home to many rare Pokémon. Rayquaza uses its power to fend off aerial threats while Latias uses her psychic abilities and speed to take on threats on the ground and in the forest. Their friendship deepens as they face challenges together and learn about each other's strengths and weaknesses.
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.
Latias could be the one to calm Rayquaza down. Rayquaza is known for its fierce nature. When Rayquaza gets angry or overly aggressive, Latias, with her gentle and empathetic nature, could soothe it. Maybe she uses her psychic abilities to communicate with Rayquaza on a deeper level and ease its temper.
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.
One idea could be that Naruto somehow gets transported to the Pokemon world. There, he meets a Rayquaza that has a special connection to his chakra. They team up to face a new threat that is endangering both the Pokemon world and Naruto's world. Naruto could use his ninja skills, and with the power of Rayquaza, they could create unique battle strategies.
One idea could be that Naruto uses his transformation jutsu (henge) to transform into Latias. He could then use Latias' abilities like flying and psychic powers to his advantage in a battle. Maybe he's in a new, strange land where Pokémon exist and has to blend in by using the henge.
One idea could be exploring how the other Pokemon in its environment react to Latias being pregnant. For example, some might be protective, while others could be jealous. Another plot could focus on Latias' journey to find a safe place to have her baby, facing various challenges along the way like avoiding hunters or finding enough food. A third option is to have a story about the bond that forms between Latias and a trainer or another Pokemon during her pregnancy, and how they support her through this special time.
One idea could be the main character being reborn as a Pikachu and having to navigate the world with its electric powers while making friends with other pokemon. Another could be being reborn as a Eevee and having the unique ability to evolve into any form at will, which causes both envy and admiration among other pokemon. Maybe the reborn pokemon has memories of being a human and uses that knowledge to outwit trainers and other threats.
Another plot could involve the reactions of their friends. Pikachu might be really curious and try to help in his own little way. And the other Pokémon friends could also offer their support in different ways, like gathering special berries that are good for Latias during pregnancy.
One possible plot could be that Latias discovers she is pregnant and has to hide from some villains who might want to harm her unborn child. She could then seek help from other friendly Pokemon or trainers.