A possible fanfiction could involve a fusion of their powers. For example, Naruto discovers a way to combine his chakra with the strange energy that Darth Nihilus wields. This new power could be used to either save the world from a greater threat or to bridge the gap between the two universes. Or perhaps Darth Nihilus, in his search for power, tries to steal Naruto's chakra, but Naruto's bond with his friends and the Nine - Tails gives him the strength to resist and turn the tables on Darth Nihilus.
One idea could be a crossover where Naruto is somehow transported to the Star Wars universe and meets Darth Vader. Maybe Naruto's positive energy and his never - give - up attitude start to make Vader question his dark path.
One idea could be a crossover where Darth Sidious discovers the world of Naruto and tries to manipulate the ninja politics for his own gain. He might see the chakra system as a new source of power to exploit.
Naruto would likely rely on his speed and powerful jutsu. His Rasengan could be a major weapon against Darth Nihilus. However, Darth Nihilus has the ability to drain life force. If he manages to get close to Naruto, it could be a big problem for Naruto. But Naruto's chakra reserves are vast, so he might be able to withstand the initial attacks.
I really like 'Darth Nihilus: The Lost Years'. This fanfiction fills in the gaps of what Darth Nihilus might have been doing during his less - known periods. It has some really interesting battles and interactions with other Sith Lords that are not in the official canon but feel very much in - spirit with the Star Wars universe.
One common theme is the clash of different power systems. Since Harry Potter has magic and Darth Nihilus has the Force, exploring how these two interact is a popular theme. For instance, in many fics, they might test which is stronger or how they could be combined.
One idea could be to have characters from Naruto end up in the world of Danmachi. For example, Naruto himself could find his way into the dungeon and his ninja skills would be put to the test against the dungeon monsters. His shadow clone jutsu could be used in interesting ways, like sending clones into different dungeon levels to scout or fight. Another idea is to have the concept of chakra introduced into the Danmachi world. This could change the way adventurers fight and level up. Maybe some of the Naruto characters could train the Danmachi adventurers in new combat techniques.
One idea could be a crossover where Naruto is somehow transported to the Star Wars universe and meets Padme. Maybe he uses his ninja skills to protect her from the Sith.
Another concept is that Naruto is sent to Middle - earth. There, he could use his ninja skills and chakra powers. He and Gandalf could team up to fight Sauron. Naruto's ability to make friends and inspire others would be really useful in uniting the different races of Middle - earth against the common enemy.
A more complex idea is that the Matrix is used to create a virtual training ground for the shinobi. They enter the Matrix to practice their skills in a more controlled environment. However, they soon realize that there are some dark secrets within the Matrix, and Naruto has to lead the way to uncover the truth and free those who are trapped inside.
Another possibility is that Naruto visits the Townsville, the city where the PPG live. He might be confused by the modern technology there compared to his own world. The PPG could teach him about it while he shows them some of his ninja skills like tree - climbing and water - walking.