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.
Sasuke could play an important role. In different universes, he might have different allegiances or powers. For example, in a universe where the Uchiha clan was never massacred, Sasuke could be a powerful leader. Kakashi is also a great candidate. His knowledge and skills could be very useful in strange universes. And Jiraiya, he could be the one guiding Naruto through the different universes, sharing his wisdom about the various changes and how to adapt.
First, come up with a unique concept for your alternate universe. It could be something like a world where ninjas use modern technology. Then, think about how the characters will be different. For Naruto, maybe he's not an orphan or he has different abilities. Next, plan out the plot. You can start with a small change in the Naruto universe and build on it. For instance, if the Uchiha clan was never massacred, how would that change the relationships and the overall story?
One great 'alternate universe naruto fanfiction' is 'Road to Ninja: Naruto the Movie - Another Side'. It presents a very different Naruto world where characters have different personalities and roles. For example, Naruto has a family in this AU which changes his whole dynamic.
Sasuke is often very popular in Naruto AU fanfiction. His complex personality and powerful abilities make him a great character to reimagine in different universes. Naruto himself is also a common focus, as writers like to explore different versions of him.
One interesting concept could be a Naruto AU where the ninja world is a modern, high - tech society. Instead of using traditional ninja tools, they use advanced weapons and gadgets. Another could be an AU where the main characters have different elemental affinities than in the original story, which would change their combat styles and relationships.
One common theme is the exploration of Naruto's character in a more romantic light. Since Naruto is a popular character, seeing him in different romantic scenarios in an alternate universe is appealing. Another theme is the power dynamics within the harem. How Naruto manages the different personalities and powers of the characters in his harem is often explored.
One interesting plot could be Naruto arriving in a universe where the Akatsuki are the heroes. He'd be so confused as he's always seen them as villains. Another could be a universe where ninjas don't exist, but he still has his powers. He'd have to figure out how to hide or use them in a completely different world. Maybe in a third plot, he travels to a universe where all his friends are his enemies, which would be a huge emotional and physical struggle for him.
One interesting plotline could be Naruto arriving in an alternate universe where the Akatsuki are the heroes. He has to figure out how to navigate this new world where his former enemies are now revered.