A good option would be to make one of the minor characters from the original Naruto series the main character. Like Iruka Sensei. Imagine Iruka during the Second Shinobi War, how he would have dealt with the horrors of war while still trying to uphold his values and protect his comrades. He could have his own journey of growth and discovery during this time.
Another possibility is to have a character who is a mix of different ninja clans. Maybe their mother was from one clan and their father from another. This character would be caught in a difficult position during the Second Shinobi War, as their loyalty would be divided between the two clans involved in the conflict. They would have to navigate through this complex situation, trying to find a way to bring peace or at least lessen the destruction of the war.
It could be an original character. For example, a young ninja from a small, unassuming clan that has been overlooked in the grand scheme of the war. But as the war progresses, they show extraordinary skills and courage, becoming a key figure in the battles.
Sasuke could also be the main character. His quest for power and revenge could be further explored in the context of the war. He might find himself in situations where he has to choose between his personal goals and the greater good of his village and the shinobi world.
Rock Lee could be an interesting main character for a Third Shinobi War fanfiction. Since he doesn't rely on ninjutsu, his unique fighting style could be a great asset during the war. We could see him face off against powerful ninjutsu users from other villages and prove that taijutsu is just as effective. Also, his unwavering determination could inspire his comrades during the dark times of the war.
He could meet the young Hiruzen Sarutobi. Naruto might learn a lot from him about the history and politics of the shinobi world at that time. They could also exchange jutsu knowledge to some extent.
It could be an original character created specifically for the fanfic. This character could be a young ninja with a unique power or backstory, like a shinobi who has the ability to control plants in combat.
It could also be a veteran ninja who has already seen a lot in their life but is still drawn into the Third Shinobi War. This character could have a complex backstory, perhaps they lost someone dear in a previous war and are now fighting to prevent the same from happening to others. Their wisdom and experience could be a key factor in the story.
Well, perhaps Naruto could find himself in the middle of a crucial battle during the Second Shinobi War. He could befriend some of the young shinobi who later become important figures. He might help them out in a difficult situation, like rescuing a group of shinobi from an ambush. This would change the course of the war in small ways and also form strong bonds with those from the past.
Well, the plot could revolve around a shinobi who has a special ability that is both a curse and a gift. During the Second Shinobi War, this shinobi is hunted by different factions because they believe his ability can be used to tip the scales of the war. However, the shinobi doesn't want to be a part of the war and is constantly on the run. In the end, he might be forced to use his ability to save a large number of people, including those from the villages that were hunting him, and in doing so, he changes the perception of his ability.
Madara Uchiha might also be a main antagonist. His goals of reshaping the ninja world could be directly opposed to what Naruto is trying to achieve with his newfound 'godlike' powers. Madara would likely see Naruto as a major obstacle in his grand plan for the shinobi world.
I think Rock Lee. He's often overshadowed by the more powerful ninjas with special abilities like Naruto and Sasuke. But during the 4th Shinobi War, his sheer determination and hard - work - based fighting style could have been explored more. He could have had some really cool moments against the stronger opponents.
Naruto would be an obvious choice. He played a major role in the original 4th shinobi war. But in a fanfic, you could explore different aspects of his character, like his internal struggles during the most intense battles.