The Akatsuki could be a likely antagonist. Since they were always a threat in the original series, in a Konoha - destroyed scenario, they might try to capitalize on the chaos and further their own goals.
There could also be internal antagonists. For example, some shinobi within Konoha who were dissatisfied with the previous leadership might try to take control during the rebuilding process, causing conflict with those who want to restore Konoha to its former glory. They could be power - hungry individuals who were waiting for a chance like this to assert their dominance.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
The Akatsuki could be likely antagonists. They are always interested in powerful ninja like Naruto. They might use some forbidden jutsu to control Naruto to further their goals of collecting the tailed beasts. Another possibility is Orochimaru. He is always looking for ways to gain power and Naruto's power would be very appealing. He could try to control Naruto to use him in his experiments or to fight his enemies for him.
Well, it could be Orochimaru. He was always up to no good and had an interest in powerful ninja. He might target Naruto and Temari to either steal their powers or use them for his evil experiments, which would surely lead to them getting hurt.
One possible antagonist could be a rogue ninja from another village. They might target Tenten for her unique weapon - handling skills, thinking they can use her to create powerful weapons for themselves. Naruto would then have to face this ninja to save Tenten.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.
It could be some rogue ninja clans that are after Karin for her special abilities. They might see her as a tool to gain power or information. For instance, a clan that specializes in blood - related jutsu might want to use Karin's unique blood - sensing ability for their own evil purposes.
The Hidden Leaf Village itself could be an antagonist. If Naruto goes evil, the village that once was his home would be against him now.
One likely antagonist could be those who fear Naruto's new power. For example, some of the traditional shinobi clans who are used to being in power might see Naruto as a threat. Another could be ancient evil forces that were sealed away long ago and now sense Naruto's god - like power as a way to break free. They might try to either corrupt Naruto or destroy him to prevent him from stopping their plans.
One potential antagonist could be a power - hungry shinobi from another village. They might view Hayate as a threat to their plans, maybe because Hayate is involved in some sort of peace - keeping mission between villages. So, they try to eliminate him. And Naruto, being the defender of his comrades, will not stand by and let that happen. There could also be a group of missing - ninjas who band together to take on Hayate, thinking he's an easy prey, but they underestimate Naruto's loyalty and strength.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.