Maybe the antagonist is an ancient and powerful clan within the Hidden Leaf itself. They have some dark secrets and believe that Naruto's presence could expose them. So they decide to lock him away as a baby to keep their secrets safe. They try to keep him hidden and under their control, but Naruto's will to be free eventually overcomes their attempts.
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.
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.
Danzo could be a great antagonist even when Naruto is a baby. He might see Naruto as a threat to his plans for Konoha's future and try to get rid of him secretly while making it look like an accident.
It could be a rogue ninja from another village who wants to capture Naruto and Ino for their own gain. Maybe he heard about Naruto's Nine - Tails power and Ino's family's special techniques and plans to sell them to the highest bidder.
A new teacher who is secretly a dark wizard could be the antagonist. They might have come to the school with the intention of stealing Twilight's powers. By locking her in the school, they can have more time to try and carry out their evil plan without interference from the outside world.
It could be Orochimaru. Since Naruto was a potential threat to his plans in the original story, if Naruto died as a baby, Orochimaru might be able to carry out his experiments and schemes more freely without having to worry about Naruto interfering in the future.
It could be Orochimaru. He has always been interested in power and Naruto's unique abilities. With Naruto sealed away, Orochimaru might see it as a chance to steal whatever power Naruto had or use his absence to further his own evil plans in the ninja world.
A corrupt leader from a political - based crossover world might be the main antagonist. He views Naruto as a threat to his power, especially with the mystery of his seal. So, he tries to either keep Naruto sealed away permanently or use the situation to gain more control over his own people by creating fear around Naruto's presence in their world.
The main antagonist could be a new character created specifically for the fanfiction. This character might be from a long - lost clan that has a grudge against the Uzumaki clan, of which Naruto is a part. Since Naruto is the last of the Uzumaki in the village, sealing him away would be their first step in getting revenge on the clan, and they would do everything in their power to keep him sealed.
It could be a new and extremely powerful ninja from a far - off land who has a vendetta against Konoha. His power might be so great that Naruto decides the only way to stop him in the long run is to seal himself away as a sort of trap for when the antagonist gets too close to achieving his goals.