It could be a result of a prophecy misinterpreted. He might believe that destroying the ninja villages is the key to fulfilling some grand prophecy that he thinks will ultimately lead to peace, not realizing the true meaning of the prophecy which has been distorted by false information.
The power balance would be completely disrupted. Without the ninja villages, there would be no organized ninja forces. This could lead to smaller groups or individuals vying for power, causing chaos everywhere.
One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.
One possible motive could be a misunderstanding. Maybe Haku was disguised as someone else who was about to attack Naruto or his friends, and Naruto reacted in self - defense without realizing it was Haku. Another could be that in this fanfiction, Naruto has been somehow corrupted or influenced by a dark force that made him lose his normal judgment and attack Haku.
It could be that his siblings have made a pact with an extremely evil entity. Naruto, with his sense of justice and loyalty to the greater good, decides that their existence in that state is too dangerous and kills them, though it would be a very difficult and heart - wrenching decision for him.
Another reason could be related to a prophecy. There might be a prophecy that Boruto will bring great destruction in the future, and Naruto, as the Hokage, feels it's his duty to prevent this at all costs. He might think that by killing Boruto, he can change the course of fate and protect the people he loves and the entire ninja world.
One possible motive could be mind control. Maybe an enemy used some powerful genjutsu on Naruto, making him lose his true self and turn against the Uzumaki clan. It's a common trope in fanfictions where the hero is forced to do something unthinkable.
One possible motive could be a major misunderstanding. Maybe Naruto was under some kind of mind - control or false information that made him believe the Uchiha clan was a threat to the village on a much greater scale than they actually were. So, in an attempt to protect the village, he took extreme action.
One possible motive could be that the angel attendant was working for an enemy force that Naruto perceived as a threat to his village. So, in order to protect his home and the people he loves, he might take such a drastic step.
Perhaps in a fanfiction where the world has been completely turned upside down. If Sasuke had been tricked into becoming an unstoppable villain who was about to destroy the entire ninja world, and Sakura was somehow aiding him (maybe under a genjutsu), Naruto might feel he had no choice but to stop them by killing. Another reason could be a broken heart. If Naruto loved Sakura deeply but she constantly rejected him and chose Sasuke, and then Sasuke and Sakura betrayed him in some way, his anger and pain could lead to such a drastic act.
One possible motive could be a misunderstanding. Maybe Naruto discovers some false information that makes him believe Konoha has betrayed him. For example, if he's wrongly led to think that the village elders are planning to harm his friends or his sensei. Another motive could be the influence of a powerful and evil entity that has somehow managed to control Naruto's mind. It could use Naruto's strength to achieve its own goal of destroying Konoha.