It could be an old enemy who has resurfaced and found a way to turn Naruto against the Leaf. Maybe Orochimaru, who has always been interested in Naruto's power, manipulates him into attacking the village. Orochimaru could use his knowledge of dark jutsu to influence Naruto's mind.
In this fanfiction, perhaps Naruto could be under some sort of mind control. Maybe an enemy has found a way to manipulate him into attacking the Leaf. It could also be a case where Naruto is misled about the true nature of the Leaf Village, believing it has committed some great wrong that warrants his attack.
In fanfiction, the idea of Naruto attacking Kushina is very uncharacteristic as they are mother - son. It could be a very dark or alternate universe scenario. Maybe in a plot where Naruto is mind - controlled or in a completely warped reality where family bonds are reversed.
Naruto would likely be deeply hurt, not just physically but also emotionally. He has always idolized his mother, so an attack from her would be a huge blow to his psyche. His trust in family and those close to him could be severely damaged.
In some fanfiction, Naruto's betrayal of the Leaf can seem plausible. It might be due to a misunderstanding, like the village turning against him despite his years of service. For example, if the village leaders suspect him of a crime he didn't commit, he could feel pushed to the edge. However, in the original Naruto series, his loyalty to the Leaf is a core part of his character.
One possible plot could be that Kakashi is under a genjutsu. In this fanfiction, an enemy ninja might have cast a powerful genjutsu on Kakashi, making him see Naruto as a threat to the village. So, Kakashi attacks Naruto, but Naruto, being the understanding person he is, tries to break the genjutsu instead of fighting back right away.
Perhaps there's a time - travel element involved. Naruto from the future, who has been through some horrible experiences, travels back in time and, in a state of confusion or rage, attacks Kushina. Or it could be that a powerful villain has the ability to manipulate Naruto's emotions and uses that power to make him turn on his mother. This would create a very complex and dark plotline that challenges the normal Naruto narrative.
In this fanfiction scenario, it could be that the zanpakuto has a mind of its own. It takes control of Naruto and forces him to attack Kakashi. The zanpakuto might be from a different dimension and is trying to create chaos in the Naruto world. Kakashi would have to rely on his ninja skills and his knowledge of various jutsu to counter Naruto's attacks and find a way to free Naruto from the zanpakuto's control.
In some fanfictions, it might be due to an alternate timeline or reality. A change in the past could lead to Kushina having different beliefs or loyalties. It could also be related to a new power or curse that affects her judgment and causes her to see Naruto as an enemy. However, this is often a very dark and dramatic turn in fanfiction stories.
Naruto might react with confusion at first. He has always wanted to be accepted by the villagers, so being attacked is the opposite of what he expected.