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.
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 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.
A powerful merchant guild in the Spice and Wolf world might see Naruto as a threat to their monopoly. They could hire assassins and use underhanded tactics to stop Naruto and Holo from achieving their goals. They would be a more subtle antagonist, using money and influence rather than brute force.
It could be an evil ninja who wants to capture the female wolf for her unique powers. Maybe he plans to use her chakra to create a powerful weapon or perform a dark jutsu.
Perhaps there's a group of hunters in the fanfic. They don't care about the wolf pup's connection with Naruto. All they see is a valuable catch. They might try to set traps for the pup and Naruto would have to outwit them to keep the pup safe. They could be motivated by money or a desire to prove themselves as the best hunters in the area.