It could be a result of some dark magic or a curse. Maybe an evil sorcerer experimented on the dog, transplanting human eyes as part of a twisted ritual. This would explain the horror aspect as it goes against the natural order.
Perhaps it's a sign of the supernatural. In some horror stories, the veil between the human world and the spirit world is thin. The dog with human eyes could be a spirit trying to cross over, using the dog's body as a vessel, and the human eyes are a manifestation of its human - like consciousness.
There was a dog with human eyes in an old, abandoned house. A group of teenagers decided to explore the place. When they entered, they saw the dog sitting in a corner. Its human - like eyes seemed to follow their every move. The eyes were so real, it was as if a human was trapped inside the dog's body. As they got closer, the dog growled in a strange way. The teens quickly left, but they all had nightmares about those eyes for weeks.
Red eyes in such a context could symbolize danger. For example, in many horror stories, a creature with red eyes often represents a threat to humans.
Maybe it was a result of some dark magic. A witch or a warlock might have cast a spell on the dog, giving it human eyes to terrify people.
In a desolate forest, a girl is camping. She hears a dog barking in the distance. As the night falls, the barking gets closer. A dog with matted fur and a strange gait emerges. The girl tries to shoo it away, but it doesn't budge. Instead, it starts circling her tent. The girl is afraid to sleep as the dog keeps making strange noises outside. In the morning, she wakes up to find the dog sitting right in front of her tent, still staring at her. She quickly packs up and leaves the forest.
Maybe it's a strange genetic experiment gone wrong. Some evil scientist in the fanfic world might have tampered with Naruto's DNA, adding some sort of aquatic - like genes that resulted in gills.
One possible storyline could be that Naruto's new 'four eyes' are a result of some strange jutsu gone wrong. Maybe he was trying to enhance his perception skills and ended up with an extra pair of eyes. These eyes could give him unique abilities, like seeing different types of chakra more clearly or even predicting an opponent's moves better. He might struggle at first to control this new change and it could be a source of both humor and growth in the story.
A possessed human might have red eyes. If a person is under the influence of an evil spirit, their eyes could turn red as a sign of this possession. This is a common trope in horror stories where the possessed person then goes on to do all sorts of terrifying things.
One possible motive could be some sort of twisted religious or cult - based belief. They might think that sacrificing humans in a slaughterhouse - like setting would please their deities or gain them supernatural powers. For example, in some fictional horror stories, cults sacrifice people believing it will open portals to other dimensions.
One possible motive could be power. Naruto's eyes might possess some unique power in this fanfic, like the ability to control a powerful jutsu or access some hidden knowledge. The thief could want to use this power for their own gain, perhaps to take over a village or defeat their enemies.
Isolation is another theme. Maybe the story takes place in a remote area where the sight of a strange 'dog - human' figure is especially terrifying. The victim is alone and has no one to turn to for help when this horrifying entity shows up. It creates a sense of helplessness.