A great plot could be that Naruto discovers he has the power of the god of genjutsu due to some ancient bloodline that was hidden from him. He then embarks on a journey to understand this power. Along the way, he uses his genjutsu to create illusions that help him train in different combat scenarios. He might also use it to communicate with the spirits of past genjutsu masters to gain more knowledge.
One interesting plot could be Naruto mastering a new and extremely powerful genjutsu that even the strongest shinobi can't break. He might use it to defeat a great enemy that was thought to be invincible. Another could be Naruto using his genjutsu god - like powers to enter the minds of his friends and heal their inner traumas.
Potential allies could be his friends like Sasuke. Sasuke, with his sharingan and combat skills, could team up with Naruto in battles against those who fear Naruto's newfound genjutsu power. Enemies might include Orochimaru. Orochimaru is always interested in powerful abilities and would likely see Naruto as a threat to his plans.
In Naruto reincarnation of Kaguya fanfiction, there could be a plot where Naruto discovers that he has the ability to open new dimensions like Kaguya did. This would give him an edge in battles but also attract unwanted attention from other powerful forces. Also, the story could revolve around Naruto trying to understand Kaguya's true motives for creating the chakra system. By doing so, he might find a way to make the shinobi world a better place, perhaps by redistributing chakra more fairly or something similar.
A great plot might involve a character who has the Fourth Dojutsu but has to keep it a secret from everyone. As they struggle with this burden, they start to realize that there are dark forces that are aware of their power and are trying to manipulate them. This creates a lot of internal and external conflict for the character.
Perhaps a plot where Naruto is influenced by an evil godlike entity. This entity could be from a different dimension. It whispers dark thoughts into Naruto's mind, gradually turning him against the values he once held dear. As a result, he starts to perform actions that are completely out of character for the original Naruto, like attacking innocent villages to gain more power.
There's also a plot where Madara and Naruto are the only two people left in a post - apocalyptic shinobi world. They must rely on each other to survive and in the process, they discover new aspects of themselves and their powers. This plot is full of action and also explores their emotional connection in a desolate setting.
Some fanfictions might focus on the psychological effects of the mind control jutsu. For example, if a character is under mind control for a long time and then is freed, how do they deal with the memories of what they did while controlled? It could be a very emotional and character - driven story. Maybe they struggle with guilt or fear of being controlled again.
Perhaps in a fanfiction, an enemy uses death magic to bring back powerful villains from Naruto's past. Naruto then has to use his own skills and newfound knowledge of death magic (maybe learned from a wise hermit) to defeat them all over again. This could lead to some really intense battles and character development for Naruto as he grapples with this new threat.
One interesting plot could be that Naruto awakens the Sharingan during a battle with a powerful new enemy. This unexpected turn gives him new abilities like predicting the enemy's moves better. Another plot might involve Naruto getting the Sharingan in a dream and then slowly learning to use it in the real world. It could also be that Naruto inherits the Sharingan from a long - lost relative, which changes the whole dynamic of his relationships in the ninja world.
Some fanfictions might have a plot where Naruto remembers a past life as a normal person in a non - ninja world. This would create an interesting contrast as he tries to adapt his ninja skills and values in a world that has no concept of chakra or jutsus. He could use his ninja knowledge to solve normal world problems in unique ways. Or, perhaps he remembers a past life as an enemy of the ninja world. This internal conflict between his current self who is a hero and his past self who was an antagonist could be a major plot point. He would struggle with the memories and the urge to not repeat the mistakes of his past life.
In some fanfictions, the brainwashing jutsu on Naruto could be part of a bigger scheme. For example, a new villainous organization wants to use Naruto as a weapon. They brainwash him and try to control his immense power. But Naruto's willpower, even under the jutsu, might start to show through in small ways, and his friends use these glimmers to figure out how to save him.