One aspect of this fanfiction could be the exploration of the harsh realities within the Naruto universe. It might show characters being forced to make difficult choices between killing their opponents or being killed themselves. This could lead to a deeper understanding of the moral gray areas that exist in a world full of ninja battles and power struggles.
Maybe Kakashi could be the one. He's always been Naruto's mentor in many ways. He has the knowledge and skills to train Naruto for such an unusual task. He could use his Sharingan to analyze the fanfiction and teach Naruto how to spot the dangerous elements within it.
A reason could be that Itachi is framed as a traitor to the Leaf Village in the fanfiction. Naruto, being the defender of the Leaf, would then see Itachi as an enemy and take action to kill him to uphold the village's safety and honor.
Well, perhaps Naruto is forced into a strange situation where he has to combat the ideas and stories in fanfiction that are causing some sort of chaos in the ninja world. Maybe some evil force is using fanfiction to distort the real story of the ninja world and Naruto is the only one who can stop it by 'killing' these false narratives.
Naruto could use his improved taijutsu skills. He might close in on Gato quickly and land a series of powerful punches and kicks that Gato can't defend against. Since Naruto is quite fast and has good reflexes, he could easily overwhelm Gato in close - combat.
One reason could be Sasuke's thirst for power. If he believes Naruto is the only obstacle in his path to ultimate power, he might be driven to kill him. In some fanfictions, Sasuke may be influenced by a dark entity that twists his mind into thinking Naruto is a threat that needs to be eliminated.