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.
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 Naruto alternate story fanfiction, Rock Lee is quite popular. His determination to succeed without relying on natural chakra abilities is inspiring. Writers often explore scenarios where he overcomes even greater challenges. Itachi is also a favorite. His tragic past and the mystery surrounding his actions give a lot of material for alternate stories. Additionally, Sakura is popular. You can develop her character further, perhaps making her a more powerful ninja earlier in the story or changing her relationship with Naruto and Sasuke.
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.
I'm not sure specifically which one is the absolute longest. There are many great alternate scenario Naruto fanfics out there. You could try searching on popular fanfic platforms like FanFiction.net or Archive of Our Own. They have extensive collections and you can usually sort by length to find some of the longer ones.
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?
The fanfiction's alternate dimension likely has different rules and settings. In the original, the ninja world has its established ways. Here, in the 'naruto x naruko alternate dimension fanfiction', there could be new types of chakra, different ways of training, or altered historical events that make it distinct from the original story.
He could meet an alternate version of himself. This Naruto might have made different choices in life, like choosing not to pursue being a Hokage. It would be interesting to see how they interact.
Power exploration is also a big theme. Different dimensions may have different power systems. So, Naruto has to learn about new types of chakra or abilities. In some fanfictions, he might even combine his original powers with the new ones from the alternate dimension. This can lead to really cool battles and power - up moments. Another common theme is friendship. Even in alternate dimensions, Naruto still values his friends. He might meet alternate versions of his friends or make new ones. The relationships he forms and how they help him through difficult situations are often explored in these fanfictions. It adds an emotional depth to the stories.
In alternate naruto fanfiction, Hinata can be extremely popular. Writers might give her a more assertive role. For example, in some stories, she could be a powerful leader instead of the shy girl in the original series. Also, Itachi is a popular choice. His complex character and the mystery surrounding his actions make him ripe for exploration in alternate storylines, such as what if he didn't have to carry out the massacre of the Uchiha clan.