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.
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.
One possible reason could be a sense of disillusionment with the village. Maybe he feels unappreciated for all his efforts in protecting Konoha. Another reason might be that he is being framed for something bad in the village and decides to leave rather than face false accusations. Also, he could be lured by the promise of a greater adventure outside Konoha that is not directly related to money.
The Hokage, whoever it is at the time, would see Naruto's actions as a major threat. They would likely assemble the ninja forces to defend Konoha. But there would also be a part of them that would wonder what drove Naruto to this. Kakashi, for example, would be conflicted. He has a deep bond with Naruto, but he also has a duty to protect Konoha. So he would try to find a way to end this without harming Naruto too much.
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.
One possibility is that Naruto could be from a hidden village that was destroyed by Orochimaru for his experiments. The survivors scattered, and Naruto ended up in the world alone. He then had to learn to fend for himself and discover his own ninja way without the influence of Konoha.