It could be Orochimaru. He is always after power and Naruto's new silent and perhaps more powerful form could be a threat to his plans, so he would try to stop Naruto.
It could be Danzo. He was always a bit of a shadowy figure in the Naruto series. In a ninja tribunal fanfiction, he could be working behind the scenes to manipulate the tribunal for his own gains, perhaps trying to get rid of those who oppose his more extreme views on protecting the village.
It could be Orochimaru. He's always been after power and new jutsu. If Naruto is guarding something really valuable, like a new powerful ninja technique, Orochimaru would be a likely antagonist. He'd stop at nothing to get his hands on it.
Perhaps it could be a powerful ice spirit that has been awakened by some dark jutsu. This ice spirit has no concept of good or evil but is causing destruction as it spreads ice everywhere. Naruto and his friends would have to find a way to either seal it or make it understand the harm it's causing. In this case, the ice spirit would be the main antagonist as it opposes the well - being of the villages.
A powerful and corrupt ninja from another village could also be the main antagonist. This ninja might be jealous of Naruto Regbinks' skills or the attention he gets. He could try to undermine Naruto Regbinks at every turn, starting conflicts between villages and trying to make Naruto Regbinks look bad in the eyes of his own people. This would create a lot of political and personal drama within the fanfiction.
It could be a long - lost relative of Orochimaru. This person might have been secretly studying Orochimaru's forbidden jutsu and developed even more terrifying techniques. They could be seeking revenge on the ninja world for ostracizing Orochimaru.
Maybe an entire rival village decides to target the prodigy. They see the potential threat that the prodigy poses to their own village's dominance, so they send their best ninjas to take the prodigy down.
It could also be a powerful and jealous ninja from another village. This ninja is envious of Naruto's growing power and popularity. He decides to create a false narrative about Naruto being a threat to all the villages and starts a war against him. Naruto would then have to prove his innocence and stop the war before it destroys the ninja world.
In 'naruto silent ninja fanfiction', a great concept might be how Naruto's silent nature affects his relationships. For example, his friends might initially misinterpret his silence as him being aloof or angry, but later come to understand it as a sign of his growth and newfound focus.
It could be a powerful and corrupted Huntsman. He might have once been a colleague of the Silent Knight but was consumed by greed for power. He now uses his skills to create chaos and try to take over the kingdoms, and the Silent Knight has to stop him.
The main antagonist could be an ancient evil spirit that has been awakened by the mixing of ninja and wizarding magic. This spirit is angry at the intrusion and starts to possess students and teachers at Hogwarts. The ninja and Harry Potter must figure out how to exorcise the spirit before it's too late and Hogwarts is completely taken over.