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.
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.
A 'locked away pokemon fanfic' could be about Pokemon that are locked away for various reasons. Maybe it's about rare or dangerous Pokemon that are locked in a secret facility to protect the world from them. Or perhaps it's about Pokemon that are unjustly imprisoned by villains and the story follows a hero's journey to free them.
It's hard to say without reading the specific fanfic. But it could be a young and brave trainer who stumbles upon the locked away Pokemon. There might also be a villain or a group of villains who are responsible for locking the Pokemon away in the first place.
It could be Danzo. He was always power - hungry and had his own ideas about how the village should be run. He might see Naruto as a threat to his plans, so he locks Naruto away as a baby. He wants to control the village without the interference of the jinchuriki's power.
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.
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.
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 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.
It would make him more resentful. Naruto is a character full of energy and a desire for recognition. Being locked away would deny him the chance to interact with others and gain that recognition. So, he would be angrier at the world that has isolated him.