Perhaps Dark Naruto as a necromancer discovers a way to use the souls of the dead to power up his own abilities. He starts collecting souls, which causes a rift between him and his former friends. He could also be on a quest to find a way to resurrect his mother using necromancy, and in the process, uncovers dark secrets about the Uzumaki clan and their connection to the afterlife.
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 plot idea could be that the dark witch and the necromancer start off as enemies. The necromancer is raising an army of the undead that is threatening the witch's forest realm. But as they clash, they discover a common enemy that is manipulating them both. So, they have to put aside their differences and work together.
One unique element is the new power set for Naruto. Instead of just his regular ninjutsu, he has necromancy. This allows him to interact with the dead in ways that are not possible in the original story. For example, he can raise the dead for information or to fight for him.
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.
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 Harry, as a dark necromancer, using his newfound powers to bring back some of the great wizards from the past to learn from them, but the magic has unforeseen consequences like attracting dark entities. Another could be that he's on a quest to revive a loved one, which goes against the natural order of magic in the wizarding world and causes a rift between him and his friends.
In a 'dark blood Naruto fanfic', the dark blood could give the wielder the ability to see the darkest secrets of others. Naruto, with his new power, uncovers a conspiracy within the ninja world that is far more dangerous than anyone thought. He has to use this power, which is feared by many, to save the world while also dealing with those who want to stop him because of his 'dark' ability.