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.
In the 'naruto locked away as a baby fanfiction', perhaps the Third Hokage is forced by some external pressure, like threats from other villages, to lock Naruto away. The village elders might also be involved in this decision. Naruto grows up alone, with only the occasional visit from a sympathetic shinobi who secretly brings him food and some basic ninja training. Naruto, not knowing the full truth, starts to resent the village. When he finally breaks free, he has to face the reality of his situation and decide if he can forgive the village and become the hero he was meant to be.
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.
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.
One possibility is that the story could focus on how the village copes without Naruto. Maybe there would be a different kind of unrest or a search for a new way to deal with the Nine - Tails' power. Without Naruto, characters like Iruka might have a different role, perhaps becoming more involved in trying to find a solution to the power void.
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 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.
One possible plot could be that Tsunade discovers baby Naruto alone and decides to take him under her wing. She could train him from a very young age, teaching him not only ninja skills but also important life lessons. Maybe she'd protect him from those who still hold grudges against the Nine - Tails within him. This would lead to a Naruto with a different kind of upbringing and a very strong bond with Tsunade.
In this fanfiction, it could be that Naruto's death as a baby is the result of a conspiracy. Maybe some anti - Uzumaki or anti - Jinchuriki group within Konoha planned his death. This would then lead to a series of events where the truth is slowly uncovered by some of the more perceptive characters in the village. This could create a lot of internal conflict as characters have to choose between loyalty to the village and uncovering the truth about Naruto's death.
One possible plot could be that Naruto is locked in a cage as a result of some dark jutsu used against him by an unknown enemy. His friends then have to embark on a journey to find the key or the counter - jutsu to free him. Maybe they face many trials along the way, and Naruto, while locked, has to struggle with his inner demons as well as the physical confinement.
Maybe in the fanfiction, baby Naruto has a nightmare. Kushina then holds him close, reassuring him that he's safe. She could tell him stories about his father, Minato, and how they both love him very much. This would comfort Naruto and he'd soon fall back asleep in her warm embrace.