Well, in fanfictions where Naruto gets controlled, Kabuto could be a likely antagonist. He is a master of various ninjutsu and medical techniques. He might see Naruto as a valuable asset and try to control him using his knowledge of the human body and chakra system. Additionally, an ancient demon or spirit sealed long ago could be the antagonist. If it manages to break free and take control of Naruto, it could use his power to wreak havoc on the ninja world.
One likely antagonist could be a new, unknown enemy. Maybe a powerful ninja from a far - off land who has heard of Naruto's power and wants to control him for his own political gain in his own village. They could have unique powers that allow them to take over Naruto's mind. Also, Danzo could be an antagonist in such a story. He has shown in the original series that he is willing to do whatever it takes to achieve his goals, and controlling Naruto would be a huge advantage for him.
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.
One likely antagonist could be a powerful new villain who has the ability to mind - control. This villain might target Deku specifically because of his potential as a hero. Another could be an old enemy of the hero society who sees Deku as a key to their revenge.
It could be the traditional villains from the original story. Maybe some of the old enemies of Percy who have a vendetta against him. For example, the Titans or some rogue demigods who oppose him for power or personal reasons.
Cell - like characters are often antagonists. Since Cell was such a major foe in the original series, new versions of Cell - like beings could be created in fanfiction to make Gohan angry. They might target his loved ones or the Earth itself, provoking Gohan's rage.
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.
Orochimaru is often a common antagonist in these types of fanfictions. He has a history of experimenting on people and his knowledge of jutsu could be used to brainwash Naruto. He might want to use Naruto's power for his own evil plans.
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.