Perhaps Naruto uses his newfound mastery of all ninja arts to defend the ninja world from a powerful and previously unbeatable enemy. He could combine different arts in creative ways to outwit the foe. For example, using water jutsu in combination with earth jutsu to create a new kind of defensive or offensive move.
It could be a group of rogue ninja who are jealous of Naruto's new powers. They might band together to try and steal his knowledge of all ninja arts or defeat him to prove their own superiority.
Perhaps Naruto discovers some dark secrets about the ninja world that make him lose faith in the ideals he once held. He then uses his skills and knowledge to create his own order, ruling with an iron fist as a 'dark master'. He could also form alliances with other anti - hero or villainous characters from the Naruto universe.
One possible plotline could be Sakura going on a solo mission to prove herself as a strong ninja, facing unexpected enemies along the way.
One possible plotline could be that the fem master chief gets transported to the Naruto universe. She then teams up with Naruto to fight a common enemy, perhaps an alien threat that has somehow made its way into the ninja world. Their different fighting styles, her high - tech combat and his ninjutsu, could make for some really cool battle scenes.
It could be a result of a prophecy misinterpreted. He might believe that destroying the ninja villages is the key to fulfilling some grand prophecy that he thinks will ultimately lead to peace, not realizing the true meaning of the prophecy which has been distorted by false information.
In some cases, the fanfiction might be a crossover with another universe where the idea of a ninja doesn't fit. So, to make Naruto fit into this new universe, the writer has to take away his ninja identity. This allows for new and interesting interactions between Naruto and characters from the other universe.
A possible plotline could be that a new enemy emerges in the RWBY world, a puppet master who starts to take over the minds of the hunters and huntresses. The RWBY team has to figure out how to stop this enemy before everyone they know becomes a puppet under the enemy's control.
One interesting plotline could be Menma's struggle to fit into a world that's different from what he's used to. Maybe he has to deal with the expectations of the villagers who compare him to Naruto.
The most exciting plotlines often involve the clones' relationships with the regular ninja. For instance, a plot where a clone befriends a young ninja trainee and they learn from each other. Then there are stories where the clone wars spill over into the civilian areas of the ninja villages, causing chaos and forcing Naruto and others to protect the innocents. Another exciting aspect is when clones start to question their purpose in life and go on a quest for self - discovery during the clone wars, which can lead to some really deep and thought - provoking storylines.
A possible plotline could be that Calypso, with her alluring powers, tries to tempt Naruto away from his path of becoming Hokage. But Naruto, with his strong will, resists and instead tries to show Calypso the importance of having a noble goal. Another plotline might be that Naruto and Calypso team up to fight a powerful entity that is causing chaos in both their worlds.