There could be internal antagonists within Naruto's own village. Some of the more conservative ninja in the village might not trust Naruto's new - found skills and powers obtained from Zetsu. They could try to undermine Naruto or even attempt to exile him, fearing that he has been corrupted by Zetsu's teachings.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.
Well, one possibility could be that Zetsu imparts some unique and dark jutsu to Naruto. Maybe Naruto starts to learn stealth and subterfuge skills from Zetsu, which are different from what he learned at the ninja academy. This could lead to Naruto having an edge in certain battles where traditional ninja skills aren't enough.
It's likely that Naruto's chakra control and power would develop in new and unexpected ways. Black Zetsu might introduce him to strange chakra - based abilities that are not part of the normal ninja training. This could give Naruto an edge in combat, but it also might make him a target. Since Black Zetsu has his own motives, Naruto could be dragged into some dangerous and complicated situations that he may not be fully prepared for.
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.