Maybe the main antagonist is a high - ranking official in the village. They see Naruto as a threat to their power or their vision for the village. They manipulate situations to make Naruto's life difficult and eventually drive him out. Once Naruto leaves, they might send other Anbu members to hunt him down to eliminate any potential threat he could pose in the future.
It could be a rogue Anbu member. This person might be jealous of Naruto's power and popularity within the Anbu. So, they spread false rumors about Naruto which lead to his decision to leave the village. This antagonist would then try to further harm Naruto while he's outside the village, using their own Anbu skills against him.
There's a possibility that the main antagonist is an external force. For instance, a powerful ninja from another village who has a vendetta against Konoha. They target Naruto specifically because he's an Anbu and they think by getting rid of him, they can weaken Konoha. Naruto leaves the village to draw this antagonist away from his home and protect the people he loves.
Perhaps Naruto in the Anbu has a personal mission that goes against the village's orders. For example, he might befriend someone from an enemy village who is actually innocent but is being targeted by Konoha. When the village refuses to listen to his pleas, he decides to leave. He'll use his Anbu abilities to protect his new friend and find a new place where they can both be safe, away from the political drama of the ninja villages.
It could be Danzo. Since he's always been a bit of a shadowy figure in the Naruto world, he might be the one behind Naruto's neglect in the village. He could have spread rumors or influenced others to keep Naruto down, and when Naruto leaves, he might send agents to stop him from becoming a threat outside the village.
The main antagonist could be an old - school ninja who believes in the traditional and often harsh ways of the ANBU. They see Naruto's actions as weakening the village and set out to oppose him at every turn, trying to bring back the old ANBU regime.
Perhaps a powerful shinobi from another village who has a special grudge against the Leaf's ANBU. He targets Kakashi and Naruto specifically because of their reputation within the ANBU. He has unique abilities that pose a great challenge to them, like the ability to nullify ninjutsu for short periods.
It could be a rogue ninja from another village who has a vendetta against Naruto. This ninja might spread false rumors about Naruto in Konoha, which eventually leads to Naruto leaving. So, this ninja would be the main antagonist as he is the root cause of Naruto's departure.
It could be some of the more conservative village elders in Konoha. They might see Naruto Namikaze's unorthodox ways and growing power as a threat to their traditional way of running the village. So they create situations that make Naruto feel unwelcome and eventually lead to his departure, making them the antagonists in the story.
Naruto might encounter a group of rogue ninjas. At first, they seem like enemies, but as he gets to know them, he realizes they have their own reasons for being outcasts. They could teach Naruto some unorthodox fighting styles that are not taught in the Leaf Village. Also, there could be a mysterious traveler who has knowledge about Naruto's family that even he doesn't know. This traveler could be the key to unlocking some hidden power within Naruto.
It could be a rogue ANBU member who has gone bad and is trying to expose Naruto's secret identity for some evil purpose.
One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.
It could be an evil shinobi who wants to capture the Kitsune Anbu for their unique powers. Maybe they want to use those powers to take over the Hidden Leaf Village. Another option is a rogue Anbu member who has turned against the village and sees the Kitsune Anbu as a threat to their own plans.