Maybe he feels betrayed. In the original story, Naruto has faced a lot of discrimination in Konoha when he was young. So in the fanfiction, it could be that some similar or new issues make him decide to hide.
One reason could be that he feels misunderstood by the villagers. Despite all he has done for Konoha, some still hold grudges or are afraid of his power. Another might be that he wants to explore the world on his own terms, away from the responsibilities and restrictions of Konoha. Maybe he also feels a sense of loneliness there, as he has lost many important people and the village constantly reminds him of those losses.
It could be that Konoha wants Naruto to use his influence to bring peace among different clans. Naruto is well - liked and respected, and his words might carry a lot of weight.
In this fanfiction, it could be that the Sith from Star Wars somehow make an alliance with the dark forces in Naruto's world. Konoha then has to rely on both their ninja skills and some newfound Star Wars - like technology or magic that has also been brought into their world. For example, lightsabers could be modified to be used by ninja, and the Force could be a new power source that some characters start to explore.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
From a security perspective, Konoha would be weaker. Naruto is a very powerful ninja, and Hinata is no slouch either. Their skills and abilities would be missed. Enemies might see this as an opportunity to attack Konoha. Also, Naruto has been a symbol of hope for the village. His departure could lead to a decrease in morale among the villagers. They might start to feel less secure and more pessimistic about the future.
It would create a sense of panic. Naruto is a very important figure in Konoha. His strength has been crucial in protecting the village. Without him, the villagers would fear attacks from other villages or threats from the Akatsuki. For instance, if the Akatsuki knew Naruto had left Konoha, they would likely see it as an opportunity to capture him more easily.
Another reason might be a lack of acceptance. Despite all his efforts, if Naruto still feels like an outcast in Konoha, he could decide to defect. He might think that he can find a place where he is truly understood and valued elsewhere.
Perhaps he discovers something about his past or his powers that makes him feel he has to leave Konoha to explore it further. For example, he might find out about a hidden place related to the Uzumaki clan and wants to go there alone to uncover the secrets. Or it could be that he has some kind of internal conflict within himself, like feeling unworthy of being in Konoha due to some self - perceived failure, and so he runs away.
Konoha might be in a state of panic. Naruto is a very important figure in the village, and his disappearance will surely make the villagers worry and fear for their safety.