A mysterious organization that has infiltrated Konoha could be the main antagonist. They spread false rumors about Naruto Namikaze, causing unrest among the villagers. Their real intention is to use Naruto's departure as a distraction while they carry out their more sinister plans within Konoha. Naruto, unaware of their full scheme, leaves Konoha thinking it's for the best.
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.
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.
In a 'Naruto Namikaze leaves Konoha' fanfic, it could be that Naruto is framed for a crime he didn't commit. The villagers turn against him, and even his friends start to doubt him. Feeling betrayed and alone, he decides to leave Konoha. As he travels, he meets other outcasts who have also been wrongly accused, and together they form a group to clear their names and seek justice.
The main antagonist could be a new character. For example, a powerful ninja from a rival village who has a vendetta against Konoha. This ninja could manipulate Naruto into leaving Konoha by spreading false rumors about the village. Then, he tries to use Naruto's power as an assassin for his own evil plans.
Maybe the main antagonist is a powerful figure within Konoha who doesn't want Naruto to leave and become an independent force. He secretly sends assassins after Naruto. When Temari gets involved, this figure also targets her. His actions are driven by his thirst for power and fear of Naruto's potential outside of Konoha's control.
The elders of Konoha could be the main antagonists. They might be the ones who have been neglecting Naruto all along, and when he leaves, they see him as a threat to Konoha's stability.
The Konoha elders could be the main antagonists. They are often shown to be quite traditional and set in their ways in the original series. If Naruto goes against their old - fashioned ideas about the village's future and ninja code, they would likely oppose him strongly and could be the driving force behind making Naruto an outcast, which in turn could lead to his 'betrayal'.
It could be Orochimaru. He has always had his eyes on Konoha and might find a way to manipulate Naruto into attacking it. Maybe he uses some new experimental jutsu on Naruto to make him do his bidding.
It could be a new villain who has been plotting against Konoha while Naruto was away.
It could be a rogue ninja from within Konoha who doesn't want Naruto to return because he fears Naruto's growing power will disrupt his own plans for power within the village.
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.