In some fanfictions, Itachi might be corrupted by a powerful and evil jutsu. This transformation makes him a danger to everyone around him, including Naruto's friends. So Naruto, out of his love for his friends and the village, decides to kill Itachi to put an end to the chaos that Itachi, in his corrupted state, is causing.
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.
Perhaps Naruto discovers something about Itachi that the rest of the world doesn't know and he needs to run away to protect that secret. It could be a powerful jutsu or a message that could change the balance of power in the ninja world.
One reason could be for strategic purposes. Itachi was a highly strategic ninja. So, in fanfiction, Naruto might act like him to outwit a particularly difficult enemy. For instance, when facing an enemy who is a master of deception, Naruto could adopt Itachi's calm and calculating demeanor to see through the enemy's tricks.
In many fanfictions, the scenario of Naruto and Itachi killing the Uchiha clan is a very interesting but also controversial topic. One aspect could be the change in Naruto's character. Usually, Naruto stands for justice and protecting others. If he were involved in such a massacre, it would be a huge deviation from his original character. Maybe in the fanfiction, there could be some extreme situations that force him to do so, like being mind - controlled or having some false information.
It could be because of a dark curse. Suppose Naruto was cursed by an ancient evil. This curse slowly ate away at his sanity and made him view his friends in Team 7 as threats. As the curse took over more and more, he finally reached a point where he killed them. However, this would require a lot of backstory and character development in the fanfiction to make it somewhat believable.
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.
One reason could be jealousy. Suppose Naruto had achieved something that Sakura deeply desired for herself or for someone she loved, and in a fit of envy, she took drastic action. But this would be a very out - of - character move for the Sakura we know from the original series.
In some fanfictions, a possible motivation for Naruto could be to prevent a greater evil. Maybe he was tricked into believing that the Uchiha clan was about to start a war that would destroy the entire ninja world. So, he thought that by taking part in killing the clan, he could save more lives in the long run.
Maybe in a fanfiction where Kakashi is mind - controlled. It could lead him to harm Naruto without his normal self - control.
It might be for the greater good. If Obito's actions in the fanfic are leading to destruction on a large scale, Konan, being a protector of sorts, decides to take him out to save the world or at least her part of it.
Maybe the friend betrayed the village in a really bad way. In the Naruto universe, loyalty to the village is important. If the friend joined the enemy and was causing great harm, Naruto could see killing them as a last resort. For instance, if they were about to give away crucial secrets that would lead to the destruction of the village.