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.
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.
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.
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 Naruto's newfound powers related to Kaguya. Maybe he has an easier time accessing certain chakra forms or has unique abilities that set him apart from other ninjas. Another plot could revolve around how the shinobi world reacts to Naruto being related to Kaguya. Some might fear him, while others might see it as a chance for greater power and unity.
One idea could be that Naruto discovers his connection to Horus and gains unique powers related to the Egyptian god. For example, he might be able to control the elements in a new way, like using the power of the sun which is associated with Horus. Another plot could involve Naruto having to face an enemy that is also related to Egyptian mythology, and his Horus - related powers are the key to victory.
Maybe the son discovers an ancient scroll left by Hashirama that contains long - lost jutsu. This sets him on a journey to master these jutsu while also facing the challenges of those who want the scroll for their own malicious purposes. He could have to team up with Naruto and his friends to protect the scroll and the village.
One idea could be Naruto inheriting Iroh's wisdom and tea - making skills. He might use Iroh's philosophical approach to deal with the conflicts in the Naruto world. For example, when facing enemies, instead of just fighting, he tries to understand their motives like Iroh would.