Well, a possible plotline might involve Naruto being possessed by the essence of the Shredder. As a result, he starts to act more like the Shredder in his own world. He could form his own group of followers similar to the Foot Clan and try to take over the ninja villages. His friends would then have to find a way to break the possession and bring back the old Naruto. Or, perhaps Naruto willingly takes on the Shredder role to gain new powers to fight a greater evil in his world, but he has to struggle with the darker aspects of the Shredder's personality.
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.
One possible plotline could be Naruto using his new position as a daimyo to bring about political reform in the ninja world. He might try to end the long - standing feuds between different ninja villages by leveraging his power.
Well, a plotline could be that Naruto is transported into Zeref's body. He has to figure out how to control Zeref's powers and deal with the people who are after Zeref. As he does this, he tries to introduce his own ideas of friendship and loyalty to those around Zeref. Maybe he even tries to find a way to end Zeref's curse of immortality using his ninja knowledge. It would be a complex story of adaptation and change.