It could be due to a conflict of interests in the fanfiction world. Suppose there is a power struggle between different factions. Kagome, Shippo and Naruto might belong to a group that believes Minato, even as a baby, will grow up to be a threat to their cause. Maybe there are some secret powers that Minato is born with that they fear will be used against them in the future. Or it could be a case of mind control where an external force is making them do this against their normal nature.
Well, perhaps in this fanfiction, there is some sort of time - traveling chaos. Kagome, from Inuyasha, and Shippo along with Naruto might be in a situation where they are forced to attack baby Minato. It could be that they are under the control of an evil entity. This entity could be using them to change the course of history for its own evil purposes. Or it could be a prophecy that they misinterpret, leading them to believe that Minato is a danger at his infancy.
One possible reason could be an alternate timeline gone wrong. Maybe some dark magic or a powerful villain has manipulated Kagome, Shippo and Naruto into thinking baby Minato is a threat to their world. Another reason could be a misunderstanding. For example, they might believe that Minato is somehow related to a future danger and they are trying to prevent it before it starts. However, this is a very dark and unorthodox scenario considering Minato is a beloved character in the Naruto universe.
One possible fanfiction could be about Kagome somehow traveling to the Naruto universe. Maybe she meets Minato and they form an alliance. And she discovers that Naruto is Minato's son. Shippo could be a unique addition, perhaps he has some special abilities that are useful in the Naruto world.
The story could end with a realization of their mistake. Once they understand that they were misled or misinformed, they could try to reverse the damage. Maybe they use some kind of time - travel or magic to fix what they've done and ensure Minato grows up as he should in the original Naruto story.
Kagome could be a foreign element that brings new magic or abilities. For instance, her spiritual powers could be used to combat certain dark forces in the Naruto world. Shippo, being a fox - demon, could have a connection with Naruto due to his own jinchuriki status. They could all bond over their unique powers and the fact that Naruto is Minato's son.
One possible plot could be that their own group betrays them. Maybe for some powerful magical item or a secret that Kagome holds. Shippo, being young and not as powerful, is easily overpowered. Kagome, on the other hand, tries to fight back but realizes she's been tricked by those she trusted. She then has to find a way to escape with Shippo and seek revenge or justice.
Perhaps in the fanfiction, Shippo discovers a special power within himself that is related to Kagome's time. This power could be the key to helping Kagome solve a big mystery. Maybe there's an ancient artifact in her time that has a connection to the feudal era, and Shippo's newfound power allows them to understand and use it to their advantage. He could also make new friends in Kagome's time and learn valuable lessons about friendship outside of the feudal era group.
Maybe he misses Naruto a great deal. Fanfiction might offer different scenarios and stories about Naruto that he finds interesting. It could also be that he wants to see how others perceive his son in fictional tales.
One possible reason could be a misunderstanding. Maybe Naruto is somehow influenced by an enemy's jutsu that makes him see Minato as a threat. For example, if an enemy uses a genjutsu to distort Naruto's perception of his father.
One possible plot could be about Minato's team training baby Naruto. Maybe they teach him basic ninja skills early on, like how to throw a kunai accurately. This could also involve some heartwarming moments between Minato and Naruto as father - son, with the team members looking on fondly.
One possible plot could be that Minato discovers baby Naruto is sick. He might use his ninja skills to search for a rare herb that could cure Naruto. Minato would face many challenges on this quest, like dangerous animals or rival ninja clans. And when he finally gets the herb, he returns to Naruto and nurses him back to health, strengthening their father - son bond.
In fanfiction, Naruto could snap at Minato due to the pressure he feels. Naruto has his own ideals and goals for the village, and if he feels that Minato's legacy or the way Minato is revered in the village is somehow hindering his own path or the changes he wants to make, he might lash out. He may think that Minato's actions, while heroic in the past, are now holding the village back in a modern context.