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.
There's a chance that the main antagonist is an ancient evil that has been awakened by the unrest in the ninja world caused by Naruto's departure from Konoha. This entity targets both Naruto and Temari because their combined power and influence could pose a threat to its plans of world domination. It uses its dark magic to create obstacles for them at every turn.
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.
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.
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 this fanfiction, perhaps Naruto leaves Konoha because he's being framed for something he didn't do. As he flees, he encounters Temari. Temari, being a strong - willed character, might be intrigued by Naruto's situation. She decides to help him clear his name. During this process, they travel to different places, learn about each other's pasts and dreams, and their relationship evolves from distrust to mutual respect and then to a deeper connection.
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.
The main antagonist could be a power - hungry elder in Temari's own village. This elder might see Temari as a threat to their authority, especially if she has been getting too much influence or support from other ninja. So, they frame her for a crime that leads to her banishment.
A power - hungry politician from one of their villages could be the main antagonist. This person might see Naruto and Temari's relationship (if that's part of the reason they are hiding) as a threat to his plans for power. He wants to use their situation to his advantage, either by forcing them to do his bidding or by getting rid of them altogether.
It could be a corrupt elder in Konoha. They might be power - hungry and see Naruto as a threat to their control. So they manipulate the situation to make Naruto the enemy.
It could be a powerful underworld lord who doesn't want Naruto to leave. This lord might see Naruto as a threat to his rule in the underworld.
Madara Uchiha could also be the main character in this type of fanfiction. Although in the original story his actions are mostly related to his grand plans for the Ninja world, in a fanfiction, it could be explored what would happen if he decided to leave Konoha specifically because of his Rinnegan and the power it holds.