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.
Maybe it's an old enemy who has returned stronger than ever. For example, Orochimaru could have found a new way to gain power and is now on a rampage to take over the ninja world. Naruto has to become the shield to stop Orochimaru's forces from invading Konoha. Orochimaru's motives are always complex and self - serving, so he makes a great antagonist in this scenario.
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.
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.
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.
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.
It could be a powerful Hollow that has somehow broken free from the normal Hollow hierarchy and is causing chaos in the Soul Society. This Hollow might have a special ability that makes it difficult for the Soul Reapers to defeat it, and Naruto, as the new Soul Reaper, has to figure out a way to stop it.
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.