It could also be due to a misunderstanding. Naruto might misinterpret some actions of humans as a threat to the entire world. For instance, if he sees the development of certain dangerous weapons or jutsu that he thinks will be misused to destroy the world, he may decide to take preemptive action by eliminating all humans to prevent that catastrophe.
Another motive might be related to some sort of dark influence. Suppose Naruto is exposed to an ancient and evil power that corrupts his mind. This power could fill him with hatred towards humanity, making him believe that destroying all humans is the only way to cleanse the world. Like in some stories where dark magic can twist a hero's good intentions.
Perhaps they are being manipulated by an outside force. An enemy of Konoha could deceive them into believing that the village is a threat to the greater good. This would lead them to take the drastic step of destruction. For example, if they are shown false evidence of Konoha planning to start a war that would cause mass destruction, they might act to stop it in what they think is the only way - by destroying Konoha.
One possible motive could be a sense of betrayal. Maybe Naruto felt constantly ostracized in Konoha despite his efforts to be accepted, and over time, that bitterness turned into pure hatred. For example, if he was always treated as an outcast by the villagers even after saving them multiple times, it could drive him to destroy the very place that never truly welcomed him.
It could be due to a prophecy misinterpretation. Suppose there is a prophecy that Naruto misinterprets as the Leaf Village needing to be destroyed for the greater good. Or perhaps he is tricked by a very cunning enemy who convinces him that the Leaf Village is the root of all the problems in the ninja world.
In such a fanfiction, it could be possible through a dark corruption of Naruto's power. Maybe the Nine - Tails' influence takes over him completely. His powers could go out of control, and with his incredible strength, he might start attacking without restraint, believing that the current world is beyond saving or redemption.
One possible motive could be to use Naruto as a bargaining chip. Itachi was a complex character with his own goals related to the safety of the Hidden Leaf Village in some ways. He might have thought that by kidnapping Naruto, he could influence the village's decisions. For example, he could try to stop certain actions the village was planning that he believed would lead to more harm. Another motive could be related to the Nine - Tails within Naruto. Itachi might have wanted to study or control the power of the Nine - Tails for his own purposes, perhaps thinking it could be a way to protect Sasuke in a different manner.
It could be that Naruto has lost his sanity temporarily. The stress of being a hero, the constant battles, and the losses he has endured might have taken a toll on his mental state. In this state of instability, he may see Sakura as a symbol of something he wants to preserve or protect, but his way of doing so is through kidnapping. Or there could be a new villain in the story who has the ability to make Naruto act out of character, and this villain's plan involves Naruto kidnapping Sakura.
Well, in some fanfiction, it could be a plot device to create a huge rift in the relationship between Sakura and other characters. If Sakura stabs Naruto, it would shock everyone. Maybe she was influenced by a dark power or an ancient curse that made her turn on Naruto. This would lead to a complex web of events where characters have to deal with the aftermath, both in terms of their emotions and the overall balance in the ninja world.
It could also be a power play. In the Naruto universe, power is a big deal. Some might frame Naruto to get him out of the way in their pursuit of power. Since Sasuke has his own group of fans in the fic, they could be used as tools to achieve this by making it seem like Sasuke is against Naruto, when in fact it's all a setup.
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.
Maybe in the fanfiction, Naruto is being controlled by some dark magic or a powerful enemy. This could force him to kidnap Lemon against his will.