It could be that the family discovers a false prophecy about Naruto bringing doom. In the fanfiction, they might be so desperate to prevent this 'doom' that they decide to kill Naruto, not realizing it was a false prophecy all along. This would add a tragic element as their fear led them to commit an unthinkable act.
The story would change the whole dynamic of the ninja world. Naruto's friends would be devastated. They might seek revenge on his family, which could lead to a civil war within the village or among different ninja clans. Also, the enemies of the village might see this as an opportunity to attack, thinking the village is now weak without Naruto.
In this fanfiction scenario, it could be that an enemy uses some sort of mind - control jutsu on Naruto's family. The family, under the control of this jutsu, doesn't recognize Naruto as their own and kills him. This would add an element of tragedy as Naruto would be killed by those he loves and trusts the most without them being fully in control of their actions. It would also open up the story for a revenge plot by Naruto's friends or other allies against the enemy who controlled his family.
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.
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.
One possible reason could be that his newfound 'godlike' powers make his family feel estranged. They might not understand his sudden transformation and the magnitude of his power, which creates a sense of fear or discomfort, leading them to ignore him.
He could also distance himself from them. Naruto might choose to avoid his family, not wanting to be around them as a way to show his anger. He could move out or stop participating in family activities.
Maybe he has some personal grudges or misunderstandings within the family in the fanfiction. It could be that something happened in the past that made him feel betrayed or unappreciated, so he refuses to offer help.
I'm not entirely sure which specific fanfiction this refers to. It could be a very dark and alternative take on the Naruto and Dragon Ball universes combined. Maybe in this fanfic, there was some sort of misunderstanding or power struggle among the characters that led to Naruto's death at the hands of his friends. However, without reading the actual fanfiction, it's hard to say for sure.
One plotline could be that Naruto was mind - controlled by a powerful villain. He wakes up to find he has killed his clan and has to deal with the shock and guilt while also trying to clear his name.