A great plot idea could be centered around a moment in the history of the tailed beasts. For example, when the Sage of Six Paths first divided the chakra into the tailed beasts. It could show how the beasts were initially perceived by the world. Another idea is to look at a moment in the history of the Hidden Sand Village. Maybe during a time when they were at war with Konoha and the events that led to the peace treaties. You could also explore a moment in the history of the Sharingan, like how it was first discovered and developed within the Uchiha clan.
One idea could be to change Naruto's initial upbringing. For example, instead of being shunned in the village, he could be secretly trained by an unknown shinobi who has a different view on the Nine - Tails. This would change his skills and how he approaches challenges in the ninja world. Another idea is to restart the story from the Chunin Exams but with different opponents and rules. It could add a new layer of excitement and unpredictability.
Another plot idea is that there's a secret group within the Naruto universe that has been experimenting with Titan shifting, and Naruto accidentally gets involved. He then has to figure out how to control this new power while also dealing with the group that wants to use it for evil. Maybe he discovers that some of his friends are also unknowingly part of this experiment, and he has to save them.
One idea could be that Naruto discovers a new and extremely powerful summoning scroll that allows him to call forth a god - like being from a forgotten realm. This being could teach Naruto a new form of chakra control that is far more advanced than what he has learned before.
Perhaps a fanfic where a crystal style user creates crystal clones that have different personalities and abilities. These clones could cause chaos in the village as they have a mind of their own. The main character then has to find a way to control them or face being exiled from the village. This would add an interesting dynamic as the character battles with their own power's unexpected side - effect.
A unique plot idea could be that Naruto's friends start to gain similar Saiyan - like powers. For example, Sasuke could develop a form that is a combination of his Sharingan and Saiyan power, which creates an interesting dynamic as they train together to master these new powers. Or perhaps, Naruto's Super Saiyan 3 form is the key to unlocking a long - forgotten prophecy in the ninja world that involves saving the entire universe from a cataclysmic event. In this way, the story could expand beyond the normal boundaries of the Naruto series.
One idea could be that Naruto discovers a hidden power within his time - space abilities that allows him to travel to alternate universes where different versions of his friends exist. For example, he might find a universe where Sasuke is the Hokage and Konoha has a completely different structure. Another plot could involve Naruto using his time - space powers to go back in time and prevent certain tragedies from happening in the shinobi world, like the Uchiha massacre.
A unique plot could revolve around a group of ninjas from different villages coming together because they all have some form of Heavenly Body Magic. They form an alliance to study and master this magic further, but face opposition from their respective villages who fear the power they might gain. This could lead to political intrigue and intense battles as they fight for their right to explore this new form of power.
One plot idea could be Dark Naruto using necromancy to bring back past villains to form an army against the Hidden Villages. He might do this to seek revenge for the way he was treated. Another could be that he uses necromancy to communicate with the spirits of his ancestors to gain powerful jutsu knowledge. For example, he could bring back the First Hokage to learn about his wood - style jutsu secrets.
One idea could be a time - travel fanfic where Naruto and Koneko are sent back in time. They have to adapt to the different ways of the past while also trying to find a way back to their own time. This would give them the chance to meet younger versions of their friends and family, and perhaps change the course of history in small but significant ways.
One idea could be Naruto exploring a new form of chakra control through meditation. He might discover a hidden power within himself that is only accessible when his mind is completely at peace. Another idea is that Naruto uses meditation to communicate with the spirits of past Hokages, getting their wisdom and guidance in a more direct way.