In a Naruto - Superman powers fanfic, perhaps Naruto gets some of Superman's powers accidentally. He struggles to control the new powers like heat vision and super speed along with his own ninja abilities. Superman, on the other hand, discovers he can use chakra in a limited way and they both have to figure out how to use these new combinations of powers effectively.
Well, from a practical standpoint, comparing the two is like comparing apples and oranges. Their universes have different rules regarding power and physics. In a fanfic, though, the writer can manipulate the story to suit their desired outcome. Maybe Naruto uses his intelligence and strategic thinking along with his chakra powers to defeat Superman. It could be that the fanfic has Superman in a situation where his powers are nullified and Naruto is able to use his ninja skills to gain the upper hand.
In a fanfic, their different origins could play a big part. Naruto, an orphan ostracized by his village at first, and Superman, an alien orphan. They could bond over their shared feelings of being alone at the start. Superman could teach Naruto about his Kryptonian heritage and how to embrace it, while Naruto could show Superman how he overcame the hatred in his village and turned it into love and loyalty.
Naruto could use his Rasengan with Superman's strength. Imagine the power of a Rasengan thrown with Superman - level force. It would be extremely destructive.
In a fanfic, there could be a scenario where Naruto and Superman start off as enemies but then realize they have a common enemy. They then team up against this new threat. During their initial fight, Superman might underestimate Naruto's speed and agility, which are enhanced by his ninja training. Naruto, on the other hand, might be initially shocked by Superman's sheer power. But as the fight progresses, they could come to respect each other's abilities and decide to work together.
Well, perhaps it could be about Naruto getting Superman - like powers. Maybe he could fly around Konoha like Superman soars over Metropolis. He might use his super strength to protect the village from threats that are too powerful for normal ninja skills.
It would be epic. They would be an unstoppable force. Naruto's speed and combat skills as a ninja, along with his ability to create clones, would work well with Superman's superpowers. For instance, Naruto could use his clones to distract opponents while Superman swoops in for the big attack.
Superman would probably win. His powers are on a god - like level. He can fly at incredible speeds, has superhuman strength that can move planets, and has heat vision. Naruto is strong, but his powers are more in the realm of ninja techniques and chakra control. In a direct confrontation, Superman's invulnerability would make it difficult for Naruto to do any real damage.
It could be Orochimaru. He's always been interested in power and new forms of jutsu. Seeing Naruto with Superman - like powers would make him want to either steal those powers for himself or find a way to use Naruto as a tool in his experiments.
A powerful dark wizard could be the main villain. He could be jealous of the clone's unique powers and want to steal them for himself. He might use dark magic to try and corrupt the clone or simply try to destroy it to prevent it from becoming too powerful.