One could imagine that in a really dark and twisted fanfiction, Naruto might be tricked into believing his mom is a threat to the village. But this completely ignores the fact that Naruto's mom sacrificed herself for the village and for Naruto. It would be a very wrong - headed and against - the - grain story.
Perhaps in some extremely dark fanfiction, Naruto is corrupted by some evil power. But this kind of plot is really against the essence of Naruto as a character. Naruto is known for his strong will and positive values, so it's very hard to justify him killing his mom in any normal sense.
If such a fanfiction exists, a possible motive could be some kind of mind - control. Maybe an enemy uses a powerful genjutsu on Naruto, causing him to lose his sense of self and attack his mom. But this is still a very far - fetched and unethical concept within the Naruto world.
One possible motive could be if his brother was somehow a threat to the village. Naruto is very loyal to Konoha, so if his brother was planning to destroy it or harm its people, Naruto might feel compelled to stop him at all costs.
In fanfiction, Naruto might kill Konoha if he's under some sort of mind control. Maybe an enemy manages to manipulate his thoughts and turn him against the village. Also, if Naruto experiences a great loss because of Konoha's actions or inactions. Say, if his friends are killed due to Konoha's negligence in protecting them, and he blames the village as a whole. Or if he realizes that Konoha's system is so corrupt that it's causing more harm than good to the world.
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.
It could be that Yagura had some secret plans that would endanger the balance among the ninja villages. Naruto, having a strong sense of protecting peace, discovers these plans and decides that eliminating Yagura is necessary. For example, if Yagura was planning to use a powerful and dangerous jutsu that could destroy multiple villages, Naruto would act to prevent it even if it means killing him.
In the 'boruto kills naruto fanfiction', a motive could be a power struggle. Boruto might believe that Naruto's power is holding back the village's growth or his own potential. He could think that by eliminating Naruto, he can bring about a new era of power in the Hidden Leaf. Also, it could be out of desperation. If Boruto is in a situation where he believes that killing Naruto is the only way to save someone he loves, like his mother or a friend, he might take such a drastic step.
One possible motive could be a misunderstanding. Maybe Hiashi mistakes Naruto for an enemy who has infiltrated the village in disguise. Another reason could be related to clan politics. If Naruto somehow gets involved in a situation that threatens Hiashi's clan interests, Hiashi might take extreme measures.
One possible motive could be that Kakuza has committed some heinous crimes against the Hidden Leaf Village. Maybe he has been involved in secret attacks on the village or has been plotting something really bad that would endanger the lives of many villagers. Naruto, being the protector of the village, would then take it upon himself to stop Kakuza by any means necessary, which unfortunately might end up in killing him.
Differing ideologies during the wizarding war. If James was seen as a threat to Snape's side (even if Snape was on the wrong side, from a moral perspective), Snape could justify killing him. For example, if James was too aggressive in fighting the Death Eaters and Snape thought it would lead to more bloodshed, he might take matters into his own hands to stop James.
One possible motive could be revenge. The Dursleys treated Harry awfully for years, so in fanfiction, he might reach a breaking point. Another could be self - defense if the Dursleys in the fanfiction were to take their abuse to an extreme level.
One possible motive could be extreme revenge. If the Muggle relative, like the Dursleys, had been particularly cruel to Harry over the years, some fanfiction writers might explore the idea of him snapping and seeking ultimate revenge. Another could be a dark magic influence. Maybe in the fanfic, Harry is exposed to some dark magic that corrupts his mind and makes him view his Muggle relative as an obstacle to be removed.