Yes, there are likely some out there in the vast world of fanfiction. Fanfiction writers often come up with unique and unexpected crossovers like this. However, the quality and popularity can vary greatly.
A 'Naruto kills Superman' fanfiction could be a complex and exciting read. Naruto would have to find a way to counter Superman's strength, flight, and heat vision. Maybe he would team up with some of his ninja comrades at first to study Superman's abilities. He could use his ninjutsu to create illusions and misdirect Superman. Once he figures out a strategy, perhaps using a combination of his most powerful jutsu like the Tailed Beast Bomb. It would also depend on the rules set in the fanfiction world, such as if there are any limitations on Superman's powers or if Naruto has any new abilities or enhancements. The story could also explore the moral implications of Naruto killing Superman, which could add depth to the narrative.
The OC could be an alien with a different kind of power set that is a threat to Superman. However, instead of fighting, the OC tries to reason with Superman. They show him the consequences of his actions through their own experiences on their home planet where a similar situation occurred, which might make Superman re - evaluate his path.
First, create a strong conflict. Since it's Dark Superman, you could have the reader oppose his extreme ways. For example, the reader could be part of a resistance group. Second, develop the relationship between the reader and Dark Superman gradually. Maybe they start as enemies but find common ground. Third, add some twists. For instance, the reader discovers a secret about Dark Superman that changes their perspective. Keep the plot moving forward and don't let it get stagnant.
One common theme is the struggle between power and morality. In the Injustice universe, Dark Superman has a very different view on justice compared to the traditional Superman. In an x reader fanfiction, the reader often has to navigate this new moral landscape created by Dark Superman's actions. Another theme could be redemption. Maybe the reader tries to bring back the good in Dark Superman. Also, themes of love and loyalty can be explored as the reader might be in a relationship with Dark Superman and has to decide whether to support his extreme methods or try to change him.
The OC could have a unique power that directly counteracts Superman's. For example, if Superman has his heat vision, the OC could have the ability to absorb and redirect energy. This would make their encounters very intense and give the OC an edge in battles.