One possible plot could be that in the yaoi fanfiction world, there are certain unspoken codes or etiquettes. Kakashi, being unaware or simply ignoring them, does something that is considered inappropriate. As a result, his punishment could range from public shaming within the fictional community to being forced to make amends in a rather difficult or embarrassing way. For instance, he might have to publicly apologize to the characters he has wronged while wearing some sort of humiliating outfit.
It could be the dominant character in the yaoi pairing. If there is a strong - willed character in the relationship, they might take it upon themselves to punish Kakashi for interfering or causing trouble.
Well, his friends might launch a rescue mission. They would use their various skills to track down where Kakashi is being held. Naruto could use his shadow clones to search different areas, while Sasuke might use his Sharingan to detect any hidden threats on the way to the rescue.
If Naruto was raised by Kakashi in fanfiction, their relationship would be very different from the original. Kakashi could teach Naruto more about the Sharingan and its secrets since he has one. Naruto might also inherit some of Kakashi's reading habits and love for Icha - Icha Paradise, which could lead to some really funny moments.
Perhaps it's an organization that wants to use Kakashi for their own evil plans. They might think that Kakashi's skills and knowledge would be useful for them. For example, they could be trying to create some sort of super - weapon and they need Kakashi's expertise in ninjutsu.
Often, in 'naruto gets trained by kakashi fanfiction', Naruto will face various challenges during the training. These challenges could be physical, like enduring intense sparring sessions with Kakashi. Or they could be mental, such as understanding complex ninja concepts. Through these experiences, Naruto not only becomes more powerful but also gains a deeper understanding of himself and his ninja path. This might also lead to him forging a stronger bond with Kakashi, which could play a significant role in future plot developments.
In some fanfictions, when Kakashi finds Naruto, it could be a situation where Naruto is in danger. Kakashi would then rescue him and from that moment on, their bond becomes even stronger. Kakashi might then focus on helping Naruto control the Nine - Tails' chakra more effectively, which would change the course of Naruto's development in the story.
One possible plot could be a dark turn in the story. Maybe Kakashi is under some kind of mind - control. He could be forced to fight Naruto by a powerful enemy who has taken over his mind. Naruto, being unprepared for such an attack from his mentor, gets killed. This would then lead to a series of events like Sasuke going on a rampage to find out the truth and avenge Naruto, and the whole ninja world being in shock as one of their most promising heroes is gone.
In this fanfiction, the plot might revolve around the relationship between Naruto and Kakashi as master and apprentice. Kakashi could be guiding Naruto not just in combat skills but also in understanding the deeper meaning of being a shinobi. They might go on special missions together where Naruto has to rely on Kakashi's wisdom and training more than his own brute strength. Also, Kakashi might share some of his own past experiences with Naruto, which would help Naruto grow both as a fighter and as a person.
One possible plot could be that Kakashi is under a genjutsu. In this fanfiction, an enemy ninja might have cast a powerful genjutsu on Kakashi, making him see Naruto as a threat to the village. So, Kakashi attacks Naruto, but Naruto, being the understanding person he is, tries to break the genjutsu instead of fighting back right away.
Well, the plot could involve Kakashi being a transfer student to Hogwarts. He might bring his ninja skills and unique perspective to the wizarding world. Maybe he'd form an unlikely friendship with some of the Hogwarts students like Harry, Ron and Hermione. His Sharingan could be an interesting addition, perhaps having some unforeseen interactions with magic.