One common theme is redemption. Since Kakashi can go back in time, he often tries to make up for past mistakes or prevent tragedies that occurred in the original timeline. For example, he might try to save a character who died before. Another theme is the changing of fates. He can change the destiny of not only himself but also of his friends and the whole village. He can use his knowledge of future events to better prepare for threats.
One possibility is that there would be a lot of reminiscing. Team Minato was Kakashi's old team. They might talk about old missions, like the one where they faced the Stone ninjas. Kakashi could share how their teachings influenced his leadership as Hokage.
Emotionally, it would be a powerful encounter. They might share their feelings about the losses they've all faced, like the death of Minato. This could strengthen their relationships and also give Kakashi new insights as Hokage on how to protect the village better.
One challenge could be dealing with the traditionalist shinobi who might not be on board with his more unorthodox methods. They may resist changes he wants to make to the village's training or governance.
The plot could be that Naruto gets a special mission to protect Kakashi's face from a group of rogue ninjas who want to steal Kakashi's identity. Naruto has to use his unique skills to fend off the attackers and keep Kakashi's face safe.
A possible plotline could be that a new enemy targets Kakashi because of his distinct face features, believing there is some hidden power in his appearance. Naruto then has to protect Kakashi. Another plotline could be a magical spell that gets cast on Kakashi's face, changing his expressions uncontrollably, and Naruto tries to find a way to break the spell.
A cool plot would be Kakashi traveling back to a time during one of the great ninja wars, say the Third Great Ninja War. He could use his knowledge of future jutsu and strategies to turn the tides of battles that were previously lost. He might also be able to save comrades who died in the original timeline, and in the process, change the future of many ninja families.
One great Kakashi Hokage time travel fanfiction is 'Kakashi's Time - Travel Redemption'. In this fic, Kakashi goes back in time and uses his knowledge to prevent some of the tragedies that happened in the original timeline. He focuses on training the younger generation earlier and making strategic changes. It's a really interesting read as it shows a different side of Kakashi's leadership and how he could have changed the course of the Naruto world if given the chance to go back.