Perhaps Naruto gets corrupted by some dark force. It changes his personality completely. He might start seeing all the people in the Hidden Leaf Village as the source of his problems. He could remember all the times he was ostracized as a child and now blames everyone for it. So in the fanfic, his hatred for everyone grows as he views the world in a new, darker light.
Perhaps in this fanfiction, Naruto discovers some dark secrets about the village. Secrets that make him feel like he's been used all along. Like the village was only using him as a weapon against their enemies. This realization could make him resent everyone in the village, thus hating everyone.
Maybe Harry has had some really bad experiences that made him bitter towards everyone. For example, he could have been betrayed by his friends multiple times.
Perhaps Harry has seen the worst in people too often. He might have witnessed so much greed, envy, and cruelty among those around him that he has lost all faith in humanity and thus hates everyone. He could be in a situation where he feels completely alone and that no one truly understands him.
It could be Naruto himself. Since he hates everyone, his actions against the people he once cared about could make him the antagonist. He might start attacking the Hidden Leaf Village or other ninja villages, making him the main source of conflict.
Well, it could be that Naruto has been betrayed too many times. Maybe he discovers that some of his closest friends have been using him all along for their own gains. So he starts to hate everyone, and the story could be about his journey of isolation and self - discovery as he tries to come to terms with his new feelings.
In the fanfic, Naruto could hate the Hokage because of some bad experiences related to past Hokages. Perhaps he discovers some dark secrets about how the Hokage office has made decisions that he doesn't agree with. It might be something like a cover - up of certain events that Naruto believes should have been dealt with more fairly.
Well, it could be that Percy has had some really bad experiences in his life that made him bitter towards everyone. Maybe he was betrayed by friends in the past, so now he just can't bring himself to trust or like anyone.
Well, it could be about how the characters in Naruto's world react to his memories. Maybe they gain a new understanding of his pain and his journey. For example, his friends like Sasuke might see how much Naruto has always cared for him, even when they were at odds.
One possible plot could be that Aphrodite is brought into Naruto's world by some sort of magical accident or a powerful villain's scheme. Her presence starts to cause chaos as she tries to spread her idea of love, which Naruto sees as a distraction from the real issues like protecting the village and maintaining peace. So he hates her for bringing this unwanted disruption.
One possible plot could be that Naruto is somehow corrupted. Maybe he's been influenced by a powerful dark force or a powerful enemy has tricked him into believing that everyone is a threat to the world he wants to protect. So, he decides to take extreme measures and kill everyone to 'create peace' in his warped sense.