What could be the main plot ideas in a 'naruto is a root fanfiction'?

Maybe Naruto leads Root on a secret mission to protect Konoha from a new, unknown threat. He could use his charisma to get the normally stoic and obedient Root members to think independently and come up with creative solutions. He'd show them that there's more to being a ninja than just following orders blindly. They might end up forming a new, more positive reputation for Root within the village.

In a 'Naruto leader of root fanfiction', Naruto could be leading Root in a new mission. He decides to focus on protecting the innocent rather than just following the orders of the village blindly. He trains the Root members in his own way, emphasizing on the importance of emotions and bonds, which is very different from what Root was used to under Danzo.

One possible reason could be that Root has some evil plans that directly threaten Naruto's friends or the village. Naruto, being the protector, has no choice but to take them down. For example, if Root was planning to assassinate the Hokage and Naruto found out, he would fight back and might end up killing some of their members.

One idea could be that members of Root are sent to infiltrate the Hidden Leaf under the guise of being friendly shinobi. They cross paths with Naruto and his friends. Naruto, being the perceptive one, senses something off about them. This could lead to a series of battles and mind games as Naruto tries to expose their true motives.

One possibility could be that Naruto is kidnapped by Root agents and forced to undergo their harsh training regime. They might try to break his spirit and turn him into a tool for their shadowy operations, but Naruto's strong will and his belief in his friends could help him resist and eventually find a way to escape.

Another plot could be that Naruto was experimented on by Root to be emotionless. He is then pitted against his old friends in a battle. His friends try to reach out to the old Naruto inside him during the fight. This leads to a series of internal struggles within Naruto as he starts to feel the faintest glimmers of his former emotions resurfacing.

Perhaps Naruto in Root has been assigned to keep an eye on Yugito for some political or strategic reason. As he gets closer to her, he discovers her true nature which is different from what he was led to believe. This new understanding makes him question his loyalty to Root and his growing feelings for Yugito. Their relationship could then be a central part of a story full of action, mystery, and romance as they try to navigate the complex world of ninja politics.

One possible plot idea could be that Naruto somehow gets transported to the Estrossa world and has to adapt to its rules and powers. He might have to learn new jutsus or abilities based on the Estrossa system.

One possible plot could be Naruto meets Scorpion and they end up having to team up against a common enemy. Maybe an organization that threatens both the Hidden Leaf Village and Scorpion's interests. Naruto's positive attitude starts to rub off on Scorpion, making him question his own dark past and motives.

One main plot idea could be Naruto struggling to fit into the Uchiha clan due to his different upbringing before. He might have to deal with the expectations of the clan while also trying to hold onto his own identity.