One idea could be exploring how the fourth sannin, if there was such a concept, might have influenced Naruto's training in a unique way. Maybe they had a special jutsu that they passed on to Naruto secretly.
A great plot for 'naruto sannin era fanfiction' would be to show how the Sannin's different ideologies started to form. Orochimaru's thirst for power might have begun with a particular event or discovery during this era. Tsunade could be shown dealing with the loss of her loved ones and how that shaped her views on life and the ninja world. Jiraiya's idea of finding the 'Child of Prophecy' might have been seeded during his experiences in the Sannin era as well.
One idea could be the new Sannin facing a powerful new enemy that threatens the entire ninja world. They have to combine their unique skills, like one being a master of genjutsu, another of taijutsu, and the last of ninjutsu, to overcome it.
Well, a really interesting plot could be that the Sannin were actually working together secretly to protect Naruto all along. They knew something about his birth that made him a target. So, Naruto grows up thinking he's just an orphan with no real connection to them, but as the story unfolds, he discovers the truth. He then has to learn how to use the combined knowledge and powers of the Sannin to face a new and powerful enemy that has been after him since his birth. This would add a whole new layer of mystery and power - up to Naruto's character.
One idea could be that the puppet sannin create a super - powerful puppet that requires the combined skills of Naruto and his friends to defeat. Maybe this puppet has the ability to absorb chakra and uses it to grow stronger.
A different plot might be about the Sannin's individual dreams and how they started to diverge. Tsunade's desire to heal and protect, Jiraiya's aspiration to write a great novel and find the child of prophecy, and Orochimaru's thirst for power and knowledge. You could show the events that led to these different paths and how they affected their relationships.
One plot idea could be that the Sannin discover a prophecy that only Naruto, Sasuke, and Sakura can fulfill. So they take the three under their wings more intensively. Jiraiya focuses on Naruto's spiritual growth, Orochimaru on Sasuke's control over his dark powers, and Tsunade on Sakura's physical and mental strength. As they train, they also uncover secrets about the ninja world that could change everything.
One idea could be exploring the backstories of minor characters during the war. For example, how the normal shinobi were feeling and what they were doing on the sidelines. Another could be a what - if scenario where a different alliance was formed among the shinobi villages.
Perhaps in the fanfiction, the Akatsuki somehow gets hold of the knowledge of Gear Fourth - like power and tries to use it against Naruto. Naruto then has to quickly master this form to not only defeat the Akatsuki but also prevent them from misusing this power for evil purposes. This could lead to some intense battles and strategic showdowns.
One interesting plot twist could be that the Sannin travel back to a time when Orochimaru was still a good - hearted ninja. They could try to prevent his fall to the dark side. This would change the entire future of the Naruto world as Orochimaru's actions had a huge impact on many events.
One idea could be focusing on a young shinobi who is an unknown hero during the war. They might use some unique and forgotten jutsu to turn the tide in crucial battles.