Perhaps Sasuke is possessed by some extremely evil entity. And Kakashi, in an attempt to stop the entity from causing more destruction, decides to kill Sasuke. It could also be that Sasuke discovers some dark secret about Kakashi that Kakashi doesn't want revealed, and in a moment of panic and self - preservation, he kills Sasuke.
Well, it could be that Kakashi is under some sort of dark spell or curse that makes him see Naruto as a threat to the village. In some fanfictions, there might be a situation where the village's safety is at stake and Kakashi believes that sacrificing Naruto is the only way to save everyone. Also, it could be a case of false information. If someone convinces Kakashi that Naruto has turned evil and is about to cause great harm, he might take the drastic step.
In this fanfiction, Kakashi could help Naruto in his training through mental conditioning as well. Naruto is often impulsive, so Kakashi may work on his patience and decision - making skills. He could use his Sharingan (if applicable in the fanfiction) to analyze Naruto's movements during training and give him detailed feedback. Moreover, Kakashi could introduce Naruto to different types of enemies and battle scenarios in a controlled training environment, which would broaden Naruto's understanding of combat and make him a more versatile ninja.
Kakashi could be initially shocked. He might not have expected Naruto to have such feelings towards him. But being Kakashi, he would probably handle it in a calm and collected manner.
He could also express his feelings through small gestures. Like sharing his favorite book, Icha Icha Paradise, with the reader. This would be a big deal for Kakashi as it's something very personal to him. He might also give the reader his headband as a sign of trust and a special connection between them. This would be a very symbolic way of showing his feelings.
Naruto could show his 'like Kakashi' traits in his mentoring style in the fanfic. Kakashi is a great mentor to his students, and if Naruto is like him, he might start to take on apprentices and teach them in a patient and knowledgeable way, passing on not just ninja skills but also important life lessons.