It could also be due to some sort of prophecy or family secret. Maybe his father believes that Naruto needs to be isolated until a certain time or event occurs. For example, if there is a prophecy that Naruto's power will become uncontrollable at a young age, his father might lock him away to prevent any disasters.
Another reason could be related to political unrest. If Naruto's father is in a difficult political situation, he may fear that Naruto could be used as a pawn. So, to prevent this, he locks Naruto away to keep him out of the political games that are being played in the ninja world.
One possible reason could be for Naruto's protection. His father might think that by locking him away, he can keep Naruto safe from the many threats in the Naruto world, like powerful enemies who might target Naruto for his special powers.
One reason could be that some in the village feared his potential as the Jinchuriki of the Nine - Tails. They might have thought locking him away would prevent him from causing chaos. Another reason could be related to those who still held grudges against the Fourth Hokage for sealing the Nine - Tails in Naruto. They took it out on Naruto by imprisoning him.
Well, in this fanfiction, it could be that Naruto is locked away by a powerful enemy of the village who wants to use him as a weapon later. Maybe Orochimaru gets his hands on Naruto as a baby and locks him in one of his secret labs. There, Naruto endures all kinds of experiments and hardships. But through his natural tenacity, he starts to develop unique abilities that are a combination of his jinchuriki powers and Orochimaru's experiments. Eventually, he escapes and has to decide whether to use his new powers for good or for revenge against the village that failed to protect him.
It could be the village council. They often make decisions for the safety of the village, and if they perceive Naruto as a threat, they might be the ones to lock him away.
It could also be due to a particularly bad encounter with someone in the village. For instance, if he was bullied severely by some older kids and he felt that there was no one to protect him. He might have thought that running away was his only option to avoid further harm.
One reason could be to explore the darker side of the Naruto universe. Writers might want to see how the characters and the world would react to such a major loss.
In this fanfiction, it's possible that Naruto is locked away as a result of a misunderstanding. His powers might be seen as uncontrollable by some in the village. They fear what he could do accidentally with his strength, so they lock him away in an attempt to keep the village safe. However, Naruto being Naruto, he would surely find a way to prove his innocence or break free in the end.
At first, Naruto might be confused and hurt. He doesn't understand why his father would do such a thing to him. He may feel betrayed since he expects his father to be a source of love and protection, not confinement.
One possible reason could be fear. Minato is a very powerful shinobi, and Naruto might be scared of him for some reason. Maybe he has heard stories about Minato that made him afraid.
In fanfictions, Naruto could run away from his family due to emotional abuse. If his family members constantly put him down, criticize his abilities, or make him feel unworthy, he'd likely want to escape. Also, if his family is involved in some political intrigue that he doesn't want to be dragged into. For instance, they might be making deals with other clans that Naruto disagrees with. Additionally, if there is a new family member introduced, like a step - sibling who is favored over him and he feels unloved, that could prompt him to run away.
Power imbalance could also be a reason. If Naruto's power suddenly goes out of control or he misjudges the Teen Titans' power levels and thinks they are a danger to his world or friends, he might take extreme actions. For example, if there's some kind of power - up in Naruto that makes him overly confident or paranoid, he could lash out at the Teen Titans thinking he's protecting something important.