Naruto is usually one of the main characters. Since it's Naruto - themed fanfiction set in a magic school, he would be at the center of the story, experiencing the magic world. Sakura might also be a main character. She could be really good at the academic side of magic in the school.
In the school of magic stories, there can be a diverse range of main characters. There could be a powerful headmaster, like Dumbledore. He is wise and guides the students through difficult times. There may also be a group of students from different houses. For example, a Slytherin student who initially seems mean but later shows his good side, and a Hufflepuff student who is always there to support and cheer on his friends. The combination of these characters with their different personalities and abilities makes the stories engaging.
If it was a crossover with 'Percy Jackson', Percy could be a main character along with the Magic School Bus gang. Percy could show them around Camp Half - Blood and they could learn about Greek mythology. Meanwhile, the Magic School Bus students could teach Percy about science and how it might relate to the magic in his world.
Well, Naruto would likely be one of the main characters, as the title implies he is the outcast in this high school setting. He would probably be the center of the story, with his journey of dealing with being an outcast and trying to fit in or change the social dynamics.
There could also be some original characters created specifically for the Akatsuki High School Naruto fanfiction. For example, a teacher who has a mysterious past related to the ninja world. This teacher could act as a mentor to Naruto and his friends, guiding them through their high school years while also teaching them valuable ninja skills and life lessons.
Sasuke could also be a main character in such fanfictions. His quest for power and knowledge could lead him to dabble in time magic. He may want to use it to change his clan's past or gain an upper hand in his rivalry with Naruto.
The Magic School Bus itself can be considered a main character in a way. It has the ability to transform into different forms to take the students to various locations, whether it's shrinking down to go inside a cell or expanding to fly into space. It's what makes all the adventures possible, and it's always there as part of the group, just like Ms. Frizzle and the students.
Typically, there could be a group of main characters. There might be a talented student who stands out in magic classes, a shy student who gradually overcomes their fears, and perhaps a mischievous character who often gets into trouble. There could also be a wise teacher who guides the students through their magical journey.
Naruto himself could be a main character in such fanfiction. Since he already has the Nine - Tails inside him, it's easy to imagine a story where he has a different kind of demon takeover. Another could be Sasuke. His quest for power might lead him to dabble in some dark magic involving demon takeovers.
Well, it could be Naruto himself, but with new abilities related to soul magic. He might be the one to discover this new form of magic and use it to protect his village in a different way.
Naruto is the key character for sure. But there could be new characters introduced in the fanfic as well. Maybe a magical being who helps Naruto understand his powers. And of course, Kakashi could still be an important figure, guiding Naruto in this new journey that combines his ninja training with his magical abilities.