It could be that Root has turned against the village in the fanfiction's storyline. Naruto, who loves his village more than anything, would see Root as a threat. If they start attacking the village or its people, Naruto would fight to defend it. His power might be too much for Root members to handle, resulting in their deaths.
Maybe in the fanfiction, Root has been brainwashing or using people in a cruel way. Naruto, with his strong sense of justice, would oppose this. He could discover that Root is behind some dark experiments on innocent villagers. In his anger and determination to stop such atrocities, he might kill members of Root.
One possible reason could be that Root has some evil plans that directly threaten Naruto's friends or the village. Naruto, being the protector, has no choice but to take them down. For example, if Root was planning to assassinate the Hokage and Naruto found out, he would fight back and might end up killing some of their members.
One possible reason could be a power struggle. If Riser somehow poses a threat to Naruto's world or his friends. Naruto, being the protector, might take extreme measures. For example, if Riser was trying to take over Konoha or steal some important ninja art. Naruto would fight to defend his village and in the heat of battle, end up killing Riser.
One possible reason could be a misunderstanding. Maybe Sasuke is framed for something really bad, and Naruto, in his anger and sense of justice, lashes out without knowing the truth. For example, if there's a false rumor that Sasuke has attacked the village again, Naruto might be quick to act.
Perhaps in this fanfic, Tsunade kills Naruto out of desperation to save the village from a perceived greater threat. If there was a prophecy that Naruto's power would lead to the destruction of Konoha in a certain way, Tsunade, in her role as Hokage, might feel it her duty to stop him at all costs. This would be a very tragic turn as Naruto is seen as a hero in the original story.
One possible reason could be a misunderstanding during a battle. Maybe there was some sort of jutsu misfire or misinterpretation of an attack. For example, if Kiba was using a new and powerful technique that Naruto didn't recognize, Naruto might instinctively go all - out in self - defense, nearly killing Kiba.
In a 'Naruto leader of root fanfiction', Naruto could be leading Root in a new mission. He decides to focus on protecting the innocent rather than just following the orders of the village blindly. He trains the Root members in his own way, emphasizing on the importance of emotions and bonds, which is very different from what Root was used to under Danzo.
It could be a miscommunication. Maybe Hinata said something that Naruto completely misinterpreted in a very negative way, like she didn't love him anymore or she blamed him for something major. This misunderstanding could be so great that Naruto loses hope and takes his life.
In such a fanfiction, perhaps Kawaki is driven by some extreme ideology. Maybe he believes Naruto's way of peace is a weakness and decides to take him out to change the ninja world in a more radical way.
Maybe the plot involves a mission where Naruto is sent to a realm that has been invaded by goblins. The goblins have a powerful magic item that they are using to gain an upper hand. Naruto has to fight his way through hordes of goblins, using his various jutsus like the fireball jutsu to clear paths. Along the way, he discovers the goblins' weakness and finally manages to kill the main goblin force, saving the day in this strange new world.
In a 'Naruto kills Gato' fanfiction, the plot could start with Gato's continued oppression in the Land of Waves. Naruto, having witnessed the suffering of the villagers, decides he's had enough. He uses his Shadow Clone Jutsu to surround Gato and his men. With a swift combination of Rasengan and his ninja skills, he takes Gato by surprise and defeats him, thus liberating the Land of Waves in a more direct and violent way compared to the original story.
In the 'kushina kills naruto fanfiction', perhaps there's a misunderstanding that leads to this extreme situation. For example, Naruto could be framed for something really bad, and Kushina, believing the false information, takes drastic action. It's a really twisted concept compared to the original story where family is so important.