Naruto is definitely one of the most popular characters. His energetic and determined personality makes him a central figure in many fanfictions set in Konoha High School. He's often the one getting into trouble and then finding solutions.
Naruto would probably be conflicted. On one hand, he has a deep love for Konoha, his home. But on the other hand, he might have been hurt by the past events that led to his departure. He could initially be hesitant, but eventually be swayed by the thought of seeing his friends again.
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.
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.
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.
Obviously Naruto has to be one of the main characters. He'd be the energetic and sometimes clumsy student who is always getting into trouble but has a heart of gold. Sakura would also be a main character, the smart and strong - willed girl who is often exasperated with Naruto's antics. And Sasuke, the cool and aloof student who has a mysterious past and is the object of many students' admiration.
In some fanfictions, there could be a plot where Hinata is a shy but brilliant student at Konoha High School. She might have a secret admirer, and it turns out to be Naruto. The story could then revolve around how their relationship develops within the high school setting, with all the typical high school drama like jealous classmates and exams.
At Konoha High School, their relationship could be shaped by school events. For instance, during a sports day. Naruto is all about winning and showing off his strength. Hinata, on the other hand, is more concerned about the team spirit. Initially, Naruto might not understand Hinata's perspective. But when he sees how her approach benefits the whole team, he realizes how amazing she is. This realization could be the start of a deeper connection between them, as he starts to respect and like her more.
Sakura would probably be very worried. She has always cared about Naruto deep down, so she might be constantly trying to find a way to bring him back. Kakashi, on the other hand, would likely understand Naruto's reasons to some extent. He might be sad but also respect Naruto's decision. As for Sasuke, if he is in the village at the time, he could be conflicted. He and Naruto have a complex relationship, and Naruto's leaving might make him realize how much Naruto actually means to him.