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.
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.
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.
Well, perhaps Naruto comes back with some super - strong new jutsu that he learned during his absence. He might show off his new power to his old friends and foes alike, leaving everyone in awe.
One possible reason could be feeling betrayed by the village leaders. Maybe they made decisions that Naruto strongly disagreed with, like how they treated certain groups or individuals. If Naruto felt that Konoha was no longer the place that stood for justice and fairness as he once believed, he might abandon it.
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 who has been secretly building power while Naruto was away. This rogue ninja might have a vendetta against Konoha and sees Naruto's return as a challenge to his plans. So he directly confronts Naruto to prove his own strength.
In some fanfictions, Naruto might return to Konoha to a cold reception because the villagers still hold grudges from his past. Maybe they haven't fully accepted his power or the chaos he sometimes brought. For example, they could be afraid of his Nine - Tails power flaring up again and causing destruction.
Another reason might be that Naruto is seeking a greater purpose. In the fanfiction, his 'godlike' state could make him realize that there are threats out there that he can't face while being tied to Konoha. He may leave to protect the world on a larger scale, believing that he can be more effective away from the village.
One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
Perhaps a dark entity from another dimension. This entity senses Naruto's powerful bloodline and wants to possess him or use his body as a vessel to enter the Naruto's world and wreak havoc. It would have otherworldly powers that Naruto has never faced before, making it a truly formidable antagonist.