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.
I don't know who the author of 'the one that got away novel' is. There are so many novels out there, and without more specific information, it's hard to determine the author.
I'm not sure specifically as there could be many novels with this title. It might be about a lost love or a missed opportunity. Maybe it's a story of someone who let a great relationship or a wonderful chance in life slip through their fingers.