One plotline could be Naruto starts in his own world, discovers a portal to the Pokemon world, and decides to explore it. He might start as a novice Pokemon trainer and quickly rise in the ranks using his ninja skills.
Maybe Naruto is already an established Pokemon trainer in the fanfiction. He gets challenged by a powerful villain who wants to use Pokemon for evil. Naruto has to use his Naruto - like determination and his Pokemon team to stop the villain. His Pokemon could also have some unique abilities inspired by Naruto's world, like a fire - type Pokemon that can use a Rasengan - like attack.
One possible plotline is that a portal opens up between the Naruto world and the Pokemon world. Pokemon start appearing in the ninja villages and causing chaos. Naruto and his friends have to figure out how to send them back while also dealing with some ninja who want to use the Pokemon for their own gain.
One plotline could be that Ash uses his ability to speak to Pokemon to solve a mystery. For instance, a group of Pokemon are acting strangely, and by talking to them, he discovers that there is a hidden force affecting them. Another could be that he has to convince a powerful and angry Pokemon not to destroy a village by communicating with it on a deeper level.
It's hard to say exactly as this is a very unusual concept for Naruto fanfiction. But perhaps it could involve a character having some sort of medical condition that causes incontinence and how they deal with it while still being a ninja. Maybe they have to hide it from their teammates to avoid being seen as weak.
One interesting plotline could be that Naruto is a reincarnation of a powerful Witcher in the Naruto world. He has latent Witcher powers that start to awaken as he grows up. As he discovers his powers, he also uncovers a conspiracy that links the Ninja world and the Witcher world. He has to use his Ninja skills and his emerging Witcher skills to solve the mystery and save both worlds from a great danger. This would involve a lot of character development, as Naruto has to balance his two identities and figure out how to use his powers effectively in different situations.
One plotline could be that Naruto is chosen by Poseidon to be his champion in the human world. He is given special powers to protect the seas and their secrets from those who would misuse them. Naruto, with his determination, uses these new powers to fight off evil forces that are threatening the ocean's balance.
A possible plotline could be Orochimaru's redemption. He realizes the error of his ways and joins Naruto in protecting the ninja world. He could use his vast knowledge of jutsu and forbidden arts to help Naruto against new threats.
One plotline might be that the Naruto universe and Lucifer's world collide. Naruto teams up with some of Lucifer's allies (or enemies) to save both worlds from a common threat. For example, a powerful demon from Lucifer's world is trying to invade the ninja world, and Naruto, with his new - found knowledge of Lucifer's powers and the underworld, has to lead the charge to stop it.
One plotline could be that Aphrodite takes an interest in Naruto because of his pure heart. She decides to bestow some of her powers on him, which gives him a new ability related to charm or attraction. This could be used in his battles, not in a traditional sense of a weapon, but more like a way to disarm his opponents mentally. For example, he could make his enemies hesitate or become distracted by his newfound allure.
One possible plotline could be Naruto being transported to a Spartan world. He has to prove himself among the Spartans. Maybe he starts as an outcast because he's different, but then he shows his amazing ninja skills and earns their respect. Another plotline could be that Spartan warriors are brought into the Naruto world, and Naruto has to train them in chakra control. It would be a mix of two different fighting styles and cultures.
One plotline could be Naruto starting from the bottom in the wrestling world. He's underestimated because of his small stature or his goofy personality, but he quickly rises through the ranks with his unique fighting style that combines ninja moves with wrestling holds.