It could be Orochimaru. He's always been interested in dark and forbidden jutsus. He might see Naruto as an interesting experiment and use some dark magic on him to turn him into a berserker just to see what chaos he can cause in the ninja world.
Maybe Madara Uchiha. Even if he's dead in the original story, in a fanfiction, he could be brought back somehow and use his powerful Sharingan abilities to manipulate Naruto's mind and turn him into a berserker. Madara has always had grand plans for the ninja world and a berserk Naruto could be a part of his new scheme.
Another possibility is a new, original character created just for this fanfiction. This character could be a powerful dark ninja who has a grudge against the Hidden Leaf Village. He targets Naruto because he knows Naruto is one of the strongest there. By turning Naruto into a berserker, he hopes to destroy the village from the inside.
It could be Sasuke. If Sasuke has turned completely to the dark side and Naruto fails to save him, Naruto might be so frustrated and angry that it starts to make him cold - hearted towards everyone. Sasuke's actions could be the trigger for Naruto's transformation.
It could be an evil spirit that wants to use Naruto's new ghostly form for its own dark purposes. Maybe it tries to control Naruto and make him do evil things.
It could be Sasuke. If Naruto becomes a wraith, Sasuke might see him as a threat to his own power - seeking goals. Sasuke could try to eliminate Naruto in this new form, thinking that Naruto is now too dangerous or has strayed from the path he believes in.
It could be Orochimaru. Since he has always been obsessed with immortality and power, he might see Naruto's new - found immortality as something he wants to steal or study. He could use his dark jutsus and his army of followers to try and capture Naruto.
It could be a new, powerful ninja from a far - off land who wants to destroy Konoha. This ninja might have a grudge against Naruto specifically and forces him to become the shield to protect the village.
Perhaps it's a jealous ninja from another village. This ninja has always been envious of Naruto's power. So when he gets the chance, he uses a dark magic to turn Naruto into a wolf. His goal is to make Naruto weak and lose his status among the ninja community.
In this fanfiction, perhaps Naruto witnesses something extremely tragic that shatters his mind and turns him into a berserker. His chakra could become wild and uncontrollable, and he might start lashing out at everyone. His friends would then try to find a way to bring him back to normal, like finding a special jutsu or an ancient relic.
Perhaps it's a rogue Shinigami who doesn't want Naruto to figure out how to control his new form. This Shinigami might fear that Naruto could disrupt the balance between Hollows and Shinigami if he becomes too powerful in his hollow state. So, he tries to stop Naruto at every turn, creating a lot of conflict in the fanfiction.
It could be Orochimaru. He has always been interested in experimenting with new forms and powers. If Naruto becomes a monster, Orochimaru might see him as a perfect specimen to study or use for his own evil plans.
Maybe the main antagonist is a dark sorcerer. The sorcerer's goal could be to use Hana's enslavement to Naruto to corrupt Naruto's positive energy. They might believe that by forcing this strange relationship on them, they can turn Naruto towards the dark side. So this sorcerer would constantly try to create more problems between Hana and Naruto.