Maybe Naruto discovers some dark secrets about the shinobi world and how humans are often driven by greed and power. This could make him disgusted. For instance, if he finds out that some of the wars were started for baseless reasons like expanding territory at the cost of countless lives. He would then start to view humans in a different, more negative light.
His relationship with his friends would be strained. For example, Sasuke might notice a change in Naruto's attitude towards him and others. Naruto may start to avoid his friends as he no longer trusts them like he used to.
Well, one possible plot could be that some humans are captured by aliens during a space exploration mission. The aliens, being curious, decide to keep the humans as pets. The story could then focus on how the humans try to adapt to their new life, communicate with their alien captors, and perhaps find a way to escape or gain some sort of equality.
One possible reason could be betrayal. If Naruto was constantly let down or betrayed by those he trusted among humans, it could lead to his hatred. For example, if his friends turned on him because of his jinchuriki status.
Well, the fanfiction could start with Captain Olimar being teleported to a human city by accident. He wanders around, confused, and catches the attention of a young journalist. The journalist decides to help Olimar and document his experience. As they interact with more people, they encounter different reactions - some are scared, some are curious. Olimar starts to learn about human emotions, which are very different from what he's used to in his own species. Along the way, he also helps the humans solve a local environmental problem using his knowledge from his own planet, and in return, the humans help him find a way back home.
One possible plot could be that Harry has been repeatedly betrayed by those he trusted, all of whom are humans. This string of betrayals causes him to gradually develop a hatred for all humans. He might then go on a journey to isolate himself from human society and seek revenge on those who wronged him.
In a 'Lion King 2 meets Humans' fanfiction, perhaps the humans are lost in the wild. The lions, led by Kiara and Kovu, find them. At first, the humans are scared, but then they notice that the lions seem to be showing signs of protection rather than aggression. The fanfiction could explore how the two species learn from each other. For example, the humans might teach the lions about some simple tools they use, and the lions could show the humans how to survive in the wild in terms of finding water sources and safe places to rest.
One possible plot could be that Optimus Prime, while protecting Earth from various threats, starts to develop a special bond with a particular human. He might save this human multiple times and in the process, begins to understand the complexity and beauty of human emotions on a deeper level. This bond could then lead to him making decisions that prioritize the safety and well - being of this human and by extension, all of humanity even more than his previous missions.
The plot could start with Naruto isolating himself from the village. He might go on a journey alone, avoiding any contact with humans. Along the way, he could encounter some non - human creatures who show him kindness, which makes him question his hatred.
A simple plot could be that a human survivor of a park disaster is being chased by other dinosaurs and hides near Rexy's lair. Rexy, for some reason, scares away the other dinosaurs instead of attacking the human. The human then starts to leave offerings of food to Rexy as a sign of gratitude. This leads to a strange friendship where Rexy allows the human to stay in its territory and protects the human from other threats in the park.
The plot could also involve the unity of the human race. Facing a common alien enemy, all countries and factions on Earth put aside their differences. Scientists worked together to analyze the alien technology and weaknesses. The military forces coordinated their efforts, sharing intelligence and resources. The civilians also played a part, by providing moral support and even some home - made inventions that turned out to be useful in the war. This combined effort of the entire human race could be what led to the victory in the first contact war.