Well, in the context of fanfiction, the writer might have been exploring a really extreme 'what - if' scenario. Maybe there was some kind of time - travel gone wrong, and Kushina from the past met Naruto in the present, but because of some muddled understanding of the future and her role in it, she ended up attacking Naruto. Or it could be that there was some dark curse placed on Kushina that made her turn on her own son. But really, it's all about the creativity (albeit a bit twisted) of the fanfiction writer.
In fanfiction, this could be due to an alternate reality or a dark twist in the plot. Maybe Kushina was mind - controlled by some powerful enemy. It's a very strange and dark concept that goes against the normal Naruto storyline where Kushina is Naruto's mother and loves him dearly.
One possibility in such a fanfiction could be that Kushina was somehow misled or deceived into believing Naruto was a threat to the village. This could be part of a grand scheme by an antagonist who manipulated her emotions and memories. Another aspect could be that Kushina was in a state of altered consciousness, perhaps due to a genjutsu or some other form of mental manipulation. However, this is all speculation as it is a very unorthodox and dark fanfiction concept.
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.
If Naruto were killed by Kushina in a fanfiction, it would completely shatter the Naruto universe as we know it. Naruto is the main character, and his death would mean the end of his journey to become Hokage and bring peace. All the relationships he had built, like with Sasuke, Sakura, and his other friends, would be left in ruins. It would also mean that the prophecy about him might not be fulfilled, leading to a darker and more chaotic future for the Hidden Leaf Village.
In some fanfictions, it could be due to a dark turn of events. Maybe Sasuke, still consumed by his thirst for power and vengeance, sees Naruto as an obstacle in his new, twisted path. Sakura, perhaps being manipulated by Sasuke, joins in. And Kakashi, unable to stop his students' descent into darkness, fails to protect Naruto.
Another possibility in this fanfiction concept could be that Sakura was under some sort of mind control. An enemy might have manipulated her into attacking Naruto. This would create a very tragic and complex storyline, as it would involve the undoing of all the positive bonds they had developed over the years.
Well, in a fanfiction, it might be due to a curse. There could be a curse placed on Naruto that slowly transforms him into Kushina Uzumaki. This curse could be related to some dark secret in the Uzumaki clan's past. Or perhaps a strange experiment by Orochimaru or another rogue ninja that goes wrong and causes Naruto to take on Kushina's form and some of her abilities.
One way it could happen is if Naruto somehow gains the ability to travel back in time. Maybe through a powerful jutsu or a unique kekkei genkai. He could then use his knowledge of future events and his combat skills to save his parents from their tragic fate.
In a possible fanfiction scenario where Naruto is killed by Gaara, it could be due to a breakdown in their understanding. Maybe a powerful and dark force has corrupted Gaara's mind, making him see Naruto as an enemy when Naruto tries to help. Gaara's sand powers are extremely strong and if he goes on a rampage without realizing who Naruto really is, he could end up killing him.
It could happen due to Naruto's strong bond with Kushina. His willpower and love for his mother are so great that they somehow manifest into a special ability. In some fanfic concepts, Naruto's unique chakra, which is a combination of his Uzumaki and Namikaze heritage, could have some latent power that he unlocks when he is at his most desperate moment to see his mother again. This power then allows him to revive Kushina.
Well, Naruto might break a bond with Kushina in the fanfiction. Maybe he finds out some dark secret about her that makes him question their relationship.
There could be a scenario where Kushina comes back to life somehow in the fanfiction. She might then play matchmaker between Naruto and Hinata, using her knowledge of Naruto to help Hinata understand him better. For example, she could share stories of Naruto's childhood that would make Hinata feel closer to him.