In a 'naruto kills everyone' fanfic, it could be that Naruto has a complete breakdown after some major catastrophe. For example, if all his loved ones are killed in a false flag operation by the village elders. He then decides that the whole ninja world is corrupt and starts eliminating everyone. But this goes against the positive themes of the Naruto franchise and would be a very controversial fanfic.
Well, it could be a dark AU (alternate universe) where Naruto is pushed to the brink. Maybe he discovers some great betrayal among his friends and village. So in his rage, he decides to take revenge and starts killing everyone. But this is a very extreme and uncharacteristic concept for the original Naruto character.
Perhaps in this fanfic, Naruto is under some kind of dark magic or mind control. This makes him lose his sense of self and his values. He might start seeing everyone as a threat and then go on a killing spree. However, it's a really disturbing idea considering Naruto is usually about friendship and perseverance in the original story.
One possible plot could be that Naruto is somehow corrupted. Maybe he's been influenced by a powerful dark force or a powerful enemy has tricked him into believing that everyone is a threat to the world he wants to protect. So, he decides to take extreme measures and kill everyone to 'create peace' in his warped sense.
It could be a way to explore the idea of power corrupting. Naruto has a great deal of power, and in this fanfic, it's showing what would happen if he lost his moral compass. It might also be a reaction to the traditional Naruto story's emphasis on friendship and community, flipping it on its head to show a very different, darker outcome.
Perhaps the council has been trying to control Naruto's power and use it for their own gain. They keep putting restrictions on him and his growth. Naruto, who values freedom and justice, realizes that as long as the council exists, the village will never be truly at peace. So he takes matters into his own hands and kills the council. This could then lead to a whole new set of challenges for Naruto, like dealing with the political fallout and trying to prove that his actions were for the greater good of the village.
Well, one possible plot could be that Naruto is betrayed by Konoha in some extreme way. Maybe he discovers some dark secrets about the village leadership that involve using him as a tool all along. This betrayal could push him to the edge and make him turn against Konoha, leading to a situation where he kills those who he feels have wronged him.
One possibility could be that Harry is under some dark magic influence. Maybe he's been corrupted by a powerful and evil spell or artifact that makes him lose his sense of right and wrong, leading him to turn on everyone. Another aspect could be that he's been betrayed so deeply by those he trusted that he snaps and decides to take revenge on everyone, believing they are all against him.
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 possibility could be that Jiraiya is under the influence of a powerful enemy's jutsu that makes him lose control of his actions and accidentally attacks Naruto. This could lead to a great deal of guilt and self - loathing for Jiraiya later.
One possible plot could be that Naruto is forced into a situation where he has no choice but to kill Haku in self - defense. Maybe Haku is under some kind of mind control and attacks Naruto relentlessly.
It could start with a rift between them that becomes unbridgeable. Sasuke might side with a group that Naruto is sworn to oppose. Their ideological differences grow to such an extent that they end up in a final battle. Naruto, with a heavy heart, kills Sasuke perhaps because Sasuke refuses to back down and his actions are endangering too many lives. This would be a tragic departure from the original story where their relationship was centered around mutual understanding and redemption.
In the 'naruto banished kills the kyuubi fanfic', it might start with Naruto being wrongly accused and banished. As he's on his own, he starts to explore his relationship with the Kyuubi more deeply. He realizes that the only way to break free from the chains that the village's treatment has put on him is to defeat the Kyuubi. So, he uses his ninja skills, combined with some unexpected twists in his chakra control, to fight and kill the Kyuubi. This would completely change the Naruto universe as we know it, since the Kyuubi is such a fundamental part of the story.