One possible interesting plot could be that Naruto discovers a new form of chakra that is related to nature spirits. This new power allows him to communicate with the forest and its creatures, giving him an edge in battles and also a new perspective on his ninja way.
In this alternate story, what if Naruto was born with a unique kekkei genkai that allowed him to manipulate time on a small scale? He could use it to predict his opponents' moves more accurately or even reverse small mistakes in battle. This would make him an even more formidable ninja and open up a whole new realm of possibilities for the story's plot.
An interesting plot could be that the alternate watch is the only thing that can stop an impending apocalypse. However, the watch has been lost in time and space. The main character has to travel through different time periods and alternate realities to find it. Along the way, they meet all kinds of strange creatures and characters, and they have to solve various puzzles and overcome many obstacles.
It could be an ancient ninja who was sealed away long ago and now breaks free. This ninja has powers far beyond what anyone in the current era has seen and has a vendetta against the Hidden Leaf Village for sealing him. He would be a powerful and menacing main villain.
For Naruto alternate story fanfiction, an interesting plot could be centered around the idea that all the tailed beasts are actually sentient beings with their own goals and desires, and they choose to work with the ninja instead of being forced into submission. So, Naruto doesn't have to fight to gain their friendship. Another plot could be that the Uchiha clan never gets massacred. Instead, they work with the village to develop new and powerful jutsu. And a different idea is that Rock Lee discovers a way to use chakra without relying on ninjutsu or genjutsu, which completely changes the way he is perceived in the ninja world.
One interesting plot could be that Naruto is born into a different clan, like the Uchiha. This would completely change his story arc as he'd have to deal with the Sharingan and the Uchiha's dark past. Another idea is if all the characters' genders were swapped. It would bring a fresh perspective on their relationships and how they interact in the ninja world.
A third plot might be an all - female alternate team with Hinata, Ino, and Temari. They are tasked with protecting a princess from another land during her visit to Konoha. Hinata's gentle fist and Byakugan, Ino's mind - transfer jutsu, and Temari's wind - based attacks would be used to fend off assassins and ensure the princess's safety.
In some naruto alternate world fanfiction, there could be a plot where Naruto travels back in time. He could use his knowledge of the future to prevent tragedies like the Uchiha massacre. He might also be able to train with the past Hokages earlier and gain different skills. This would change the course of the entire Naruto world, and his relationships with characters like Sasuke and Sakura would be very different as a result.
One idea could be that Naruto finds himself in a universe where the Akatsuki are the heroes. He has to figure out how to co - exist or even join them to get back to his own universe. Another plot could be Naruto entering a universe where everyone has a different elemental chakra, like some have sound - based chakra instead of the usual five. A third idea is that he hops into a universe where the shinobi world is a utopia, but there are hidden secrets that are threatening to destroy this perfect world and he has to help.
In the 'naruto juubi alternate universe fanfiction', it would be interesting if the characters' relationships were reversed. Like Sasuke could be the one trying to protect Naruto who has the Juubi's power, because he realizes that Naruto's power is the key to a new world order that could benefit all ninjas.
Another interesting plot twist might be that the White Fang, instead of being a completely antagonistic force, has a group within it that wants to work with the Huntsmen and Huntresses. They realize that their violent methods are not achieving their long - term goals and they approach Team RWBY and the others to form an alliance. This would completely change the dynamics between the characters and the story's view on the Faunus - human conflict.
In some alternate naruto fanfiction, there might be a scenario where Naruto was raised in a different village. Imagine if he was brought up in the Sand Village. His personality and skills would likely develop differently, influenced by the Sand's culture and fighting styles. He might form different relationships and have different goals compared to his original story.