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.
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.
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.
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.
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.
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.
Another plot could involve the villains from both worlds. Orochimaru from Naruto might be interested in the strange powers and experiments in Deadman Wonderland. He could form an alliance with some of the bad guys there. Meanwhile, the heroes from both universes have to come together to stop this dangerous union. They would have to combine their different fighting styles and strategies to face this threat.
A plot that stands out is when Hashirama, through Edo Tensei, has to team up with modern - day ninjas against an ancient evil that has been resurrected. It's interesting because it combines the old - school power of Hashirama with the new techniques of the current ninja generation.
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.
A plot where Danzo fakes his death and teams up with Naruto undercover to take down a hidden threat to the village. They have to keep their alliance a secret from everyone, including the other village leaders. This creates a lot of tension and secrecy in the story.
One interesting plot could be that when they time travel, they end up in a time before the Uchiha massacre. Itachi could then try to change things with Naruto's help, and in the process, their relationship deepens in a yaoi way. Maybe Naruto helps Itachi see a different path for the Uchiha, and they grow closer as they face the challenges together.