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.
Some interesting plots in RWBY alternate fanfiction could involve an alternate reality where the Dust doesn't exist. This would completely change the way combat and technology work in Remnant. Hunters and Huntresses would have to rely more on their physical abilities and semblances. Or there could be a story where Team RWBY is formed much earlier in their lives, like as children, and they grow up together facing different challenges than in the original story. There could also be a fanfic where the world of Remnant is invaded by an outside force from another dimension, and the RWBY characters have to adapt quickly to this new threat.
In some fanfictions, Tobi's alternate personality might be related to a hidden past or a connection to a long - lost shinobi clan. This could lead to a whole new backstory for the character and add depth to his motives in the Naruto universe.
One idea could be a what - if scenario where Naruto becomes a rogue ninja. This would completely change the dynamics of the story and his relationships. For example, he might be hunted by his former friends, and we could explore his inner struggle and reasons for turning rogue.
One interesting plot idea could be that in the alternate timeline, Tony Stark never becomes Iron Man. Instead, he devotes his life to clean energy research and Pepper Potts takes on a more superhero - like role, using Stark tech to fight crime. Another idea is that the Avengers lose the Battle of New York in this timeline, which leads to a dystopian world where the Chitauri rule, and the remaining heroes have to form an underground resistance.
A plot idea could be that Naruto discovers a new, ancient form of chakra that has been lost for centuries. He then has to train to master this chakra while also dealing with the political implications within the Hidden Leaf Village. Some elders might be against him exploring this new power for fear of the unknown, but Naruto, being Naruto, is determined to master it for the good of the village.