It's really hard to say. Minato is extremely fast with his Flying Raijin and is a very intelligent fighter. But Naruto has an incredible amount of chakra, his Sage Mode, and his Six Paths powers. If Naruto can get close enough to Minato, his brute strength could overpower Minato. However, Minato's speed and strategic mind might keep Naruto at bay.
In some 'minato vs naruto fanfiction', there could be a scenario where they battle in a different dimension. Minato uses his Flying Raijin to quickly move around and Naruto counters with his shadow clones and massive Rasengan attacks. Also, a scenario where they fight not as enemies but in a friendly spar to teach Naruto some secret family jutsu that only Minato knew would be really cool.
It could also be related to a prophecy or a pre - determined fate in the fanfic's plot. There might be some kind of dark prophecy that says Kawaki has to kill Naruto to prevent a greater evil. Or perhaps Kawaki is being controlled by an external force that has a vendetta against Naruto and uses Kawaki as a tool to carry out the murder.
There are many out there. A really good one might focus on the emotional reactions of Team Minato. For example, Minato might be proud of Naruto's strength and how he overcomes Pain. Kakashi could be in awe at Naruto's new techniques. Their reactions can enhance the overall viewing experience in the fanfiction.
One common theme is friendship. Writers often explore how Himawari and Kawaki, who come from different backgrounds, form a bond of friendship. Another theme is growth. They both grow as characters, learning from each other.
Kawaki makes his appearance in Boruto manga at a specific point, but I can't recall exactly. You might want to check the official manga sources for the precise chapter.
You can try looking on popular fanfiction websites like FanFiction.net or Archive of Our Own (AO3). They usually have a wide range of Naruto - related fanfictions, and you should be able to find some with the 'Team Minato Watches Naruto vs Pain' concept.