Perhaps in this fanfiction, Sarutobi is trapped in a genjutsu created by a rogue ninja. Naruto, being highly resistant to genjutsu due to his Uzumaki blood, manages to break into the genjutsu world. There, he has to fight his own inner demons as well as the rogue ninja's illusions to free Sarutobi.
One popular storyline could be the apprentice learning unique jutsu from Naruto. For example, they might learn his Rasengan technique in a more in - depth way, with Naruto guiding them through every step of the process.
I really like 'Naruto, Sasuke and Sarutobi: A New Beginning'. In this fanfic, it starts with Sarutobi having a premonition about the future of Naruto and Sasuke. So he takes steps to guide them differently. It's an interesting take on their relationship. 'Sasuke's Redemption under Sarutobi' is also good. It shows Sasuke trying to make amends with the village with Sarutobi's guiding spirit in mind. And 'The Hidden Power of the Trio' is a fanfic that gives a new perspective on the powers they possess and how they can be combined for the greater good.
In this type of fanfiction, it's possible that the story delves into Naruto's backstory and how being Sarutobi's son would have affected his childhood. Maybe he would have grown up with more guidance and support, which could have changed his personality. Instead of being the lonely outcast that he was in the original story, he could have been more confident from the start. The fanfiction might also introduce new characters related to Sarutobi that play important roles in Naruto's life. There could be new adventures and challenges that are unique to this new family dynamic, such as Naruto having to uphold the Sarutobi family name and legacy within the Hidden Leaf Village.
Perhaps he uses some ninja techniques like a shadow clone jutsu. He could make multiple clones to help him sort through and complete the paperwork quickly.
There could be. Fanfiction is a vast realm where all sorts of ideas are explored. However, I'm not sure if there is a highly popular or mainstream 'naruto is kisame apprentice' fanfiction. It might be a more niche concept, but it's entirely possible that some creative writer has delved into this idea to create an interesting story about Naruto learning from Kisame, perhaps incorporating Kisame's unique fighting style and view of the ninja world into Naruto's growth.
First, know the Naruto universe well. Understand the rules of chakra, the different ninja clans, and the existing jutsu. This knowledge will make your story more believable. For example, if your apprentice is from the Uchiha clan, you need to know about their Sharingan abilities.
Naruto would probably be extremely hurt. He has always looked up to Sarutobi as a leader and a father figure. His first reaction might be disbelief, unable to accept that Sarutobi would do such a thing. Then he would likely feel a great sense of anger and betrayal. He might lash out and try to prove his innocence.
One of the popular characters paired with Sarutobi is Jiraiya. They are both important figures in the Hidden Leaf and their relationship, whether it's as comrades or as teacher - student in some fanfic interpretations, is always interesting to explore.