The antagonist could be Orochimaru. He has always been interested in Naruto's power, especially the Nine - Tails. Maybe he has found a new way to control Naruto and has taken him away from Konoha. Orochimaru's motives would be his never - ending thirst for power and knowledge. He could be using Naruto as a guinea pig for some new and dangerous experiment related to the tailed beasts.
Madara Uchiha could be the antagonist in this fanfiction, even if he's supposed to be dead. He could have somehow found a way to come back and has set his sights on Naruto. Madara might think that by controlling Naruto, he can finally achieve his ultimate goal of creating a new world according to his own vision. He would be a formidable opponent as he has vast knowledge of ninjutsu and his Sharingan abilities are extremely powerful.
It might be a new, unknown group of rogue ninjas. They could be after Naruto because they believe that his power can be used to overthrow the current ninja world order. They see Konoha as the symbol of that order and by taking Naruto, they can both gain his power and strike a blow to Konoha. This group would be highly organized and have their own set of unique and dangerous ninja techniques.
One possible plot could be that Konoha Village has to reclaim Naruto after he has been lost in a mysterious dimension. The villagers might realize his importance more than ever and send out a team of elite ninjas, including Sasuke and Sakura perhaps. They would face numerous challenges in this other dimension, like strange new jutsus and powerful enemies. Along the way, they would also discover new things about Naruto's powers that even he wasn't aware of.
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 rogue ninja from within Konoha who has embraced the 'darkness' fully and wants to reshape the village according to his own twisted ideals.
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.
It could be a long - lost relative of one of the old villains like Orochimaru. Maybe this person has been in hiding, training and growing in power, and now wants to take revenge on Konoha for what happened to their family member.
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 antagonist could be a new, self - proclaimed ninja god who wants to rule over all the villages. He sees Naruto as the only threat to his power, so he used a powerful spell to take away Naruto's godlike abilities. Konoha wants Naruto back to stop this tyrant. This antagonist might have an army of brainwashed ninja at his command.
Perhaps it's an old enemy who has somehow managed to come back stronger. Maybe someone from Orochimaru's old experiments that went wrong, but instead of dying, they gained some dark and powerful abilities. They see Naruto's return as a threat to their plans of world domination, so they target Konoha first. They might be able to control dark chakra in a way that no one has seen before, and use it to create chaos and destruction. They could also have some minions who are equally as powerful and loyal to them, making them a formidable foe for Naruto and Konoha.
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 a neighboring village who has a vendetta against Konoha. This ninja might see Naruto's return as an opportunity to take on the strongest ninja in Konoha and prove his own strength.