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 mother, Kushina, could also be part of the family that wants him back. She was a kind - hearted and strong - willed woman. If she were alive in the fanfiction, she would be desperate to have her son with her. She would want to protect Naruto and share all the things she didn't get to when he was growing up, like teaching him about their Uzumaki heritage.
Jealousy could be a motive. Maybe Naruto's growing power and popularity within the village make his family members jealous. So they decide to kill him to end his rise.
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.
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.
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 might try to prove himself. Naruto could focus on becoming stronger and more successful as a ninja. By showing his family that he can achieve great things and that he's a good person, he hopes to change their minds. For example, he might take on difficult missions and complete them with excellence.
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.
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.