Perhaps Kabuto wants to use Naruto as a pawn in his own schemes. He might think that by reviving Naruto, he can control the situation in the shinobi world to his advantage.
It could be that Kabuto has a change of heart. Maybe he realizes the importance of Naruto in bringing balance to the shinobi world and decides to revive him as a way to atone for his past wrongs. Another possibility is that there is some greater power or entity forcing Kabuto to revive Naruto for a specific purpose that is yet to be revealed in the fanfiction.
In the fanfiction, Kabuto might revive Naruto because he sees Naruto as the key to stopping a greater evil. He may have foreseen a threat that only Naruto can face. Or maybe Kabuto has some sort of personal vendetta against another character and believes that Naruto's revival will disrupt their plans. Also, it could be related to some ancient prophecy that Kabuto believes in, where Naruto's revival is a necessary step for the future of the shinobi world.
One possible reason could be for protection. Maybe Naruto is hiding his true identity from an enemy who is specifically targeting him. He might be using the mask as a disguise to blend in and gather information without being recognized.
Well, one possibility is that Naruto might initially be deceived by Kabuto. Since Kabuto is quite cunning. Naruto could be led into situations that are against his normal moral code, but eventually he might realize Kabuto's true intentions and try to turn things around.
One reason could be to weaken Naruto. In the ninja world, being a girl might come with certain social limitations that could hold Naruto back. Another reason could be for experimentation. Madara is always interested in power and knowledge. By turning Naruto into a girl, he might be testing out some new jutsu or power - related concept. It could also be a form of psychological warfare. Madara knows Naruto has strong relationships with his friends, and this change could disrupt those relationships and cause chaos within Naruto's circle.
Maybe Itachi saw Naruto as a potential force for good in the ninja world. He might have thought that giving Naruto the Sharingan would make him strong enough to protect the village and bring peace.
In a Naruto kills Kabuto fanfiction, it would likely have a big impact on Naruto's character development. Naruto is usually about saving and redeeming his enemies. Killing Kabuto would be a departure from his normal values. This could lead to internal conflict within Naruto. He might struggle with guilt or question his own actions. On the other hand, it could also show his growth in a different way, that he's willing to do whatever it takes to protect his friends and the village. And from a plot perspective, it would create a rift between Naruto and those who believe in second chances, like Tsunade.
Well, in a fanfiction, the writer can bend the rules of the original Naruto universe. Maybe Kabuto could kill Naruto if he somehow got hold of a super - powerful and unexpected weapon or jutsu that nullified Naruto's abilities.
A 'naruto meets kabuto fanfic' could start with Naruto sensing an unusual chakra signature which turns out to be Kabuto. Naruto would be ready for a fight, but Kabuto might hold up his hands in surrender. They could then have a conversation where Kabuto reveals some secrets about the past, like some hidden experiments of Orochimaru that could still pose a danger. Naruto might then decide to keep Kabuto under watch or try to convince him to use his knowledge for good.
Naruto might also use some of the special items or powers he has acquired in the fanfiction world. Maybe he has a magical amulet that can nullify Kabuto's attacks for a short time. He uses this opportunity to dash towards Tsunade and get her to safety. Then he could use his own natural skills like his agility and reflexes to keep Kabuto at bay until help arrives.
One common theme is the transformation of Naruto. Through Kabuto's training, Naruto often becomes more versatile in his skills. Another theme is the exploration of Kabuto's motives. Why does he train Naruto? Is it for personal gain or some greater good?
A frequent theme is also the exploration of Kabuto's backstory. Fanfictions often dig deeper into his past, his relationship with Orochimaru, and how that has shaped him. Additionally, the theme of alliances and betrayals is common. Given Kabuto's history of switching sides, crossovers often play with the idea of who he will side with in new and different situations. This can lead to some really interesting plot twists.