It could be someone who doesn't like the idea of Aayla serving Naruto. Maybe a rival of Naruto who sees Aayla as a way to get to Naruto or disrupt his life.
There might be a character from Aayla's past, like an old enemy or someone from her former group who wants to bring her back. This person could see her serving Naruto as a betrayal and thus become the antagonist. They might try to force Aayla to leave Naruto's side by any means necessary, including attacking Naruto. In the process, Naruto would have to protect Aayla and their relationship would grow stronger.
Perhaps there is a magical or special circumstance. For example, a spell was cast on Aayla that binds her to Naruto as a servant. In this fanfiction, Naruto might initially be hesitant about having a servant, but as time goes on, they develop a unique relationship. Aayla could use her own skills and knowledge to help Naruto in his adventures, like providing information about certain enemies or places she has been.
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 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.
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.
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.
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.