One possible plot could be that Naruto is somehow caught in a powerful jutsu accident that was originally meant for someone else by his parents. Maybe they were trying to protect the village from a great threat and miscalculated the jutsu's range or power. This could lead to Naruto's untimely death and then the story could explore how his parents deal with the guilt and grief, as well as how the village reacts to losing Naruto, who was seen as a hero in training.
In the fanfic, Naruto could die from an unexpected illness. His parents, who have been watching over him in spirit, are devastated. They might try to find a way to communicate with the living to tell them how special Naruto was. The mourning process could involve them seeing how the village comes together to remember Naruto, with his friends and comrades sharing stories of their adventures together. This would make his parents realize the kind of person Naruto had become and how much he meant to everyone.
Sasuke would be deeply affected. He and Naruto had a complex relationship, from being rivals to friends. He would likely feel a sense of guilt, as if he should have been there to protect Naruto. Sakura would be heartbroken. She had always cared for Naruto, and seeing him die in such a tragic way in front of his parents would make her feel helpless. His parents, on the other hand, would be in utter despair. His father might feel like he failed as a father again, not being able to protect his son this time either.
Perhaps Naruto is poisoned by a powerful new villain. His parents are revived just in time to see him succumb to the poison. This event could trigger a series of events where his friends and the entire village vow to avenge his death. His parents might then decide to stay in the living world to help in this quest for vengeance, despite the rules of the afterlife.
It could be that in a special mission, Naruto discovers a hidden jutsu that allows him to communicate with the spirits of his deceased parents, leading to a touching reunion.
Perhaps Naruto has always felt different from others in the village. And when he finally learns about his parents, he realizes that their actions, even if they were for a good cause like protecting the village, still made his life very difficult. He might be angry that they didn't find a better way to handle things so that he didn't have to suffer so much growing up.
Their relationship would be centered around their mourning. They would constantly talk about Naruto, sharing memories and regrets. This could lead to a deeper, more empathetic relationship as they both try to make sense of the loss. They might also start to see each other in a new light, as they both have different perspectives on Naruto's life and death, and through sharing these, they grow closer as a couple.
His relationship with his parents would be loving. Minato would be a strict but fair father, teaching Naruto about ninjutsu and the responsibilities of being a shinobi. Kushina would be the warm, affectionate mother, always there to comfort and encourage Naruto. They would support his dreams and be proud of his every achievement.
It might make him more distant from his friends at first. He could be so consumed by his anger towards his parents that he withdraws from his usual social circle. For example, he might avoid spending time with Sasuke or Sakura because he is too preoccupied with his feelings about his parents.