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.
The main antagonist could be a dark force that is corrupting the ninja world from within. It starts to possess many powerful ninjas and turn them against their own villages. Naruto, seeing that he might be the next target and that his power could be used against the world if he is possessed, seals himself away to protect the world from this dark force.
One possible plot development could be that the village is in great danger from an enemy too powerful to defeat directly. Naruto, seeing no other way, seals himself away to act as a last - line - of - defense deterrent. If the enemy tries to completely destroy the village, Naruto's sealed power could be unleashed to counter them.
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 long - lost Uchiha with powers beyond that of Madara. This Uchiha could have been in hiding, gathering power and knowledge, and his ultimate goal is to reshape the world in his own dark image. Naruto realizes that the only way to stop him is by sacrificing himself.
It could be an evil version of Sasuke. Maybe he has fallen completely to the dark side and manipulates Naruto into destroying Konoha. Or it could be Orochimaru who has found a new way to control Naruto's actions from the shadows.
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.
Maybe an organization that specializes in using the Sharrigan for malicious purposes. They don't want Naruto to expose their secrets, so they send their Sharrigan - users to hunt him down. This organization could be made up of power - hungry individuals who will stop at nothing to achieve their goals.
Maybe a new character could be the main antagonist. A powerful and mysterious being that Luigi stumbles upon during his escape. This character might have some vendetta against the Mario brothers or just be generally evil and wants to stop Luigi's journey for its own malicious reasons.
Kabuto could be an antagonist as well. He is a power - hungry character. If Naruto is trying to bring positive change to the Akatsuki, Kabuto's thirst for power and his underhanded tactics could put him in direct conflict with Naruto, as he might see Naruto as a threat to his own plans within the Akatsuki.
The main antagonist could be some dark wizards who want to use the dragon for their evil purposes. They might be after the dragon's scales, which are valuable in making powerful dark magic items, or its fire, which can be harnessed for destruction. They would oppose Hermione's attempt to move the dragon away as it would thwart their plans.
The main antagonist could be a powerful ghost who has a vendetta against Danny. Maybe it's a ghost that Danny defeated before, but who has come back stronger and is now seeking revenge. This ghost could hunt Danny down as he runs away, causing all sorts of trouble for him.