Naruto might initially try to reason with those who betrayed him. He would want to understand why they did it. But if they refuse to listen or continue to be hostile, he would start to distance himself from Konoha. He could become a lone wolf, using his skills and power to survive on his own while still trying to figure out how to clear his name and get revenge if necessary. He would also likely feel a sense of betrayal towards the friends he thought he had in Konoha.
Naruto's reaction could vary depending on the circumstances. If he has people he still trusts in Konoha, like some of his close friends, he might try to work with them secretly to expose the real traitors. However, if he feels completely alone, he might leave Konoha altogether and seek refuge elsewhere. He could end up becoming a sort of anti - hero, with his own moral code but no longer having any loyalty to Konoha. He might also use his influence with other villages or allies he has made over the years to put pressure on Konoha to explain their actions.
He would probably be very angry. Naruto has always been a free - spirited person, and being experimented on against his will would be a huge violation of his rights. He might initially try to resist physically, but as the situation gets more complex, he could start to plot his escape and revenge.
At first, Naruto is likely to be heartbroken. Konoha has been his home, and he has always longed for acceptance from the villagers. So being abandoned would be a huge blow to him.
Naruto would likely be extremely hurt. He has always considered the Konoha 11 as his friends and comrades. So, at first, he would probably be in denial, trying to figure out what went wrong. He might try to talk to them, to understand their reasons.
At first, Naruto would be completely shocked. He has always seen Hinata as a loyal friend and someone who has deep feelings for him. So the idea of her betrayal would be hard to fathom. He might try to deny it at first.
Konoha would likely see him as a major threat. They would mobilize all their resources to stop him. This could lead to epic battles between Naruto and the shinobi of Konoha. In the process, a lot of destruction could occur in and around the village.
He might initially try to prove his innocence. He'll gather evidence or find people who can vouch for him. But as the situation worsens, he could become angry and more determined to find out the truth and expose those who are behind his false accusation. He might even leave Konoha to seek answers and allies elsewhere.
Konoha might be in shock at first. They have always relied on Naruto to some extent, and his refusal to help is completely unexpected.
The villagers would likely be shocked. Naruto is a hero to many in Konoha, and Tsunade is the Hokage. Their sudden departure would cause a great deal of confusion and concern. Some might think that Konoha is in danger if two such important figures have left.
The storyline would likely start with Naruto's disillusionment with Konoha. His actions would then shock his friends. Sasuke, for example, might initially be confused but then choose a side. There would be intense battles within the village as Naruto tries to fight against the forces that he now opposes. His former friends and comrades would be torn between loyalty to the village and their friendship with Naruto.
In some fanfics, Naruto initially tries to reason with the people of Konoha. He believes that there has been a misunderstanding and he wants to clear his name. But when he realizes that no one is listening, he becomes angry and frustrated. He might start to lash out at those who are hunting him.