His father, Minato, could be a likely candidate in a really dark fanfiction. Maybe he was resurrected in an imperfect way and his mind was warped, causing him to turn on Naruto.
Perhaps in a very strange and twisted fanfiction, Naruto's future son or daughter from an alternate timeline comes back and for some convoluted reason, decides to kill him. This would be a very unexpected and complex plot point.
His mother, Kushina, might also be involved. If she was somehow influenced by a powerful and evil genjutsu (illusion technique), she could be made to believe that Naruto was a danger and thus kill him.
His father, Minato, could be one. Maybe there's some time - travel or alternate reality situation where Minato has been corrupted in some way and Naruto has to fight him to set things right.
Iruka could step in. He has always been like a mentor and a father figure to Naruto. He was the first one to really see Naruto's potential and give him the recognition he deserved. So in the absence of his family, Iruka would be a likely candidate to fill that family - like role.
He would most likely meet his father, Minato Namikaze, and his mother, Kushina Uzumaki. These are the two main family members he never really got to know growing up.
He would most likely meet his parents, Minato and Kushina.
Maybe Kakashi could be the one. He's always been Naruto's mentor in many ways. He has the knowledge and skills to train Naruto for such an unusual task. He could use his Sharingan to analyze the fanfiction and teach Naruto how to spot the dangerous elements within it.
One possible reason could be jealousy. If Naruto has the rare Mokuton ability, his family might be jealous of his potential power and neglect him out of spite.
Maybe there are secrets in the family. For example, his parents might be involved in some dangerous and secretive missions that require them to keep their distance from Naruto to protect him, but Naruto misinterprets it as neglect.
One aspect of this fanfiction could be the exploration of the harsh realities within the Naruto universe. It might show characters being forced to make difficult choices between killing their opponents or being killed themselves. This could lead to a deeper understanding of the moral gray areas that exist in a world full of ninja battles and power struggles.
Well, perhaps in this fanfiction, Naruto's family was brainwashed by an enemy. They no longer recognized Naruto as their own and instead saw him as a threat to their new 'false' ideology. So they decided to kill him. This would completely shatter Naruto's image of family as something warm and loving, and would be a really cruel take on the Naruto universe.
Perhaps his family consists of a group of fellow banished ninjas who become his surrogate family. There could be a strong - willed female ninja who becomes his partner, and together they have a child. And also an old sage - like figure who acts as the family's wise elder, guiding them through the difficulties of living in exile.