His Sharingan - if he had it in this godlike state - would allow him to see through illusions in Skyrim. Many of the mages in Skyrim use illusions to deceive their opponents. Naruto could easily counter that. Also, his chakra control could be used to enhance his weapon handling in Skyrim. He could infuse his chakra into a sword or an axe, making it more powerful and able to cut through tougher enemies.
Well, perhaps Naruto is somehow transported to the world of Skyrim and is banished from a particular region in Skyrim due to being an outsider with strange powers. Maybe the local mages see his chakra as a threat and exile him. He then has to find a way to prove himself or find a new place to belong in this strange new world.
Well, one possible plot could be that Naruto arrives in Skyrim and his ninja skills give him an edge in the battles there. He might start as a stranger in the land and gradually gain a reputation among the different factions.
A common theme is the clash of cultures. Naruto comes from a very different world than Skyrim, and when combined with the harem element, there are often misunderstandings and interesting cultural exchanges. For example, Naruto's ninja code might be different from the values in Skyrim.
He would likely interact with the Dragonborn. They could have an interesting exchange of skills, with Naruto showing off his Rasengan and the Dragonborn demonstrating shouts. He might also meet the various Jarls in the different holds, trying to understand their leadership styles which are different from the Hokage in Konoha.
It could be a powerful Thalmor agent. The Thalmor are often seen as the bad guys in Skyrim, and if Naruto shows up, they might see him as a threat to their plans of domination. They could use their influence to get Naruto banished and then try to hunt him down.
A cool plot could be that the Sage of Six Paths in Naruto's world had a connection to Skyrim long ago. When Naruto unlocks some hidden power within himself, it accidentally triggers a link to Skyrim. Once in Skyrim, he discovers that his chakra is linked to the dragon shouts. He has to go on a quest to learn more about this connection. He meets the mages in the College of Winterhold, who are fascinated by his chakra abilities. Together, they try to figure out a way to use Naruto's power to stop a great evil that is threatening both Skyrim and, through the link, Naruto's own world.
One possible plot could be Naruto getting transported to Skyrim. He might be mistaken for a strange new race at first. As he explores Skyrim, he could use his ninja skills to fight the dragons. Maybe he teams up with the local warriors and teaches them some of his jutsu in return for learning about Skyrim's magic. His ability to move quickly and stealthily would give him an edge in the dangerous world of Skyrim.
In this crossover, Naruto might bring the concept of chakra into Skyrim. He could teach the locals how to sense and use it. His godlike status could mean he has an unlimited supply of chakra and can perform the most powerful jutsus without tiring. For example, his Rasengan could be a new and devastating weapon against the dark forces in Skyrim.
One of the most creative crossovers could be the use of Naruto's jutsu in the Skyrim world. For example, the Sharingan could be used to detect hidden traps or enemies more easily in Skyrim's dungeons. Another cool crossover would be having Naruto characters take on the roles of different Skyrim factions. Maybe Naruto could be a part of the Thieves Guild, using his speed and stealth skills from his ninja training. Also, imagine Sasuke using his Chidori in a battle against a dragon in Skyrim. It would be an epic showdown of different fictional powers.