There might be a group of rogue spirits who see Naruto as a threat to their existence. They form an alliance to oppose Naruto. They could try to manipulate the living to go against Naruto, creating all sorts of problems for him in his ghostly state.
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.
Perhaps a powerful ninja who has a grudge against Naruto even in his ghost form. This ninja might be jealous of Naruto's new powers and wants to destroy him. They could set up traps and use dark jutsu to try and get rid of Naruto the ghost.
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.
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 another powerful time - manipulating ghost. This ghost might see Danny as a threat to his own plans of ruling over all time periods. He would try to stop Danny from fully understanding and using his new powers.
It could be Orochimaru. He is always seeking power and the strange and powerful abilities of the Ghost Rider might be something he desires. He could try to capture or study the Ghost Rider to gain an edge in his own plans for power and immortality.
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.