There could be other ninja in the village who have their own nin animals too. Some of them might be minor characters that help to build the world of the fanfiction. They could show different ways of interacting with their nin animals compared to Naruto, which in turn could influence Naruto's own relationship with his nin animal.
The sensei characters like Kakashi could also be important in the fanfiction. He might give Naruto advice on how to train and bond with his nin animal. And then there could be antagonists who target Naruto because of his powerful nin animal. They could be new villains created specifically for the fanfiction.
Obviously Naruto is one of the main characters. His nin animal would also be a main focus. There might also be his friends like Sasuke and Sakura who interact with Naruto and his nin animal in different ways. Maybe Sasuke is initially jealous of Naruto's unique nin animal.
In some fanfictions, the nin animal could have a connection to an ancient prophecy. So Naruto has to figure out how to use his nin animal in relation to this prophecy to save the village. Maybe the nin animal has a hidden form that is only revealed when certain conditions are met.
The nin wolf could make Naruto more respected among his peers. Other characters might see Naruto as having an even greater potential with this powerful ally by his side. Some might be a bit jealous, like Sasuke, who could see Naruto's nin wolf as another way Naruto is getting stronger faster.
Kimimaro could be an interesting missing nin character to explore in fanfiction. He was a tool for Orochimaru, but had his own internal struggles. You could write about his life before fully becoming a missing nin, his loyalty to Orochimaru despite his own deteriorating health, and what might have happened if he had broken free from Orochimaru's control. Another character could be Nagato. Before he became Pain, he had experiences that could be considered as leading towards a missing - nin - like existence. His views on peace and his use of the Akatsuki could be delved into in the context of a missing nin story.
Sasuke is often a popular character in such fanfictions. His initial departure from the village makes him a prime example of a missing - nin. Writers like to explore his journey further, what he experiences outside the village, and how his relationships change.
Danzo could be a great antagonist. He always had his own secretive and often unethical plans. He might see Naruto as a threat even if he's innocent and frame him as a missing - nin to get rid of him.
Since I haven't read it, I can't say for sure. It could be an original character created specifically for this fanfiction, or it might be a male character from the Naruto series that has been given a new and different role as the 'last male nin'.
The nin wolf might be a gift from a powerful ninja in the fanfiction. Maybe as a sign of Naruto's growing power or a new mission he has to undertake. It could also be a wild creature that Naruto tames during his travels.
One popular original character could be Hiro. He's a medic nin who is a bit of a rebel. He doesn't follow the traditional medic nin rules and instead experiments with unorthodox healing methods. His methods are initially frowned upon, but as he starts getting results, he gains a following among the younger medic nins. Another is Nami, a shy but highly skilled medic nin. She has a special bond with animals and often uses her knowledge of animal healing to develop new techniques for human healing. And there's Taro, a strong - willed medic nin who was born in a small village and travels to the big ninja villages to share his unique knowledge of a local - only healing art.
I think Hinata would be a main character too. If she was an animal, she might be a little rabbit, shy but with hidden strength. Her love for Naruto could be shown in different ways as an animal. And Shikamaru, as a sloth - like animal, could use his intelligence to solve problems in this new animal - filled Naruto world. Gaara, with his connection to the sand, could be a desert - dwelling animal like a scorpion, adding a new dimension to his character.
It could be a rogue hunter nin who doesn't like the idea of Naruto, an outsider, joining their ranks. This rogue hunter nin might see Naruto as a threat to their power and influence within the group.