A really interesting plot could be that an old, powerful Pokemon relic has been discovered. Ash and Professor Juniper embark on a journey to study it. However, a group of villains also wants the relic for their own malicious purposes. Ash and Professor Juniper must not only protect the relic but also figure out its true nature and powers.
Perhaps Ash has a strange dream about a powerful Pokémon that only Professor Juniper seems to have some knowledge about from ancient texts. They team up to try and find this Pokémon, but they have to compete with a rival group who also want to get to it first. In the process, Ash learns a lot from Professor Juniper's wisdom and research skills.
One way is through a crisis situation. Let's say a powerful and dangerous Pokemon is on the loose. Ash and Professor Juniper have to work together to calm it down. During this process, they learn about each other's strengths and weaknesses. Ash sees Professor Juniper's courage and intelligence in handling the situation, and Professor Juniper admires Ash's determination and connection with Pokemon. This mutual admiration can lead to a stronger relationship.
One interesting idea is that a group of rogue ninjas in the Naruto world steal some of the Pokemon professor's research. They think they can use it to gain power over both the Naruto world and the Pokemon world. So, the professor teams up with some Naruto heroes to get the research back and prevent chaos from ensuing. As they work together, they learn a great deal about each other's worlds and abilities.
One idea could be a story where a young trainer teams up with Professor Sycamore to research a new and mysterious Pokemon species that has been causing strange phenomena in the Kalos region. They embark on a journey filled with challenges and unexpected encounters.
Well, a plot could involve Ash and Grace traveling through time. They might end up in the past where they meet the ancestors of some of the Pokemon they know. They could learn about the origin of certain Pokemon types and use that knowledge to help in the present. Also, a story where they are on a quest to find a rare Pokemon that can grant wishes. Along the way, they face many obstacles and make new friends among the Pokemon and other trainers.
Perhaps a plot where Fennel is researching a particular Pokemon's behavior and Ash helps her in the field. They might encounter some problems with a group that wants to use the Pokemon for not - so - good purposes. They then have to work together to protect the Pokemon and complete Fennel's research.
One plot idea could be Ash getting the ability to shapeshift accidentally. For example, he touches a strange Pokemon or an ancient artifact. Then he has to figure out how to control this new power while on his journey to become a Pokemon master. Another idea is that an evil organization wants to use Ash's shapeshifting ability for their own nefarious purposes, so he has to avoid them and protect his friends.
Maybe Ash's father was part of an ancient Pokemon - protecting clan. In the fanfiction, Ash starts to have strange dreams about his father and these dreams are actually memories passed down through some sort of psychic Pokemon connection. This leads him to search for the clan and learn more about his heritage and his father's role in it. It could involve Ash having to prove himself worthy to the clan.
One plot idea could be that Ash and Ashley team up to compete in a special Pokemon tournament that has never - been - seen - before rules. They have to combine their skills and the unique abilities of their Pokemon to overcome various challenges. Another idea is that they discover a new type of Pokemon in a mysterious forest and have to protect it from an evil organization that wants to use it for bad purposes.