A plotline might involve Naruto being found as a baby and raised as an animal by someone who doesn't understand his true nature. As he grows, he starts to show signs of intelligence and power that shock those around him. Or perhaps the village, after some event, decides to treat him like an animal, stripping him of his rights and forcing him to live on the outskirts. This could lead to a story of him trying to regain his humanity and respect in the eyes of the villagers.
One common plotline is the 'gender - bender' confusion. Naruto wakes up one day as a girl or is magically transformed, and then has to deal with the shock and the reactions of his friends. Another is the love triangle or romance aspect. Since he is now treated like a girl, different characters might develop romantic feelings for him, or he might develop new feelings for someone. There could also be a plotline about him trying to prove himself in a world that now views him differently. For example, he has to show that just because he is treated like a girl doesn't mean he is any less of a ninja.
One common plotline is Naruto being forced into battles against his will. Since he's treated like a weapon, the people in charge just send him into dangerous situations without considering his own desires. Another is Naruto trying to break free from being seen as a weapon. He might rebel against those who are using him and try to find his own path where he's valued as a person.
Often, there could be a situation where Naruto has some sort of mental setback. Maybe he forgets all his skills and knowledge, and as a result, the people around him start treating him as if he were a baby. They would then have to reteach him basic things like walking and talking in a ninja - context.
One common situation could be that the other characters in the fanfiction might constantly over - protect Harry. For example, they don't let him take any risks or do things on his own, like going to the Forbidden Forest even for a small exploration. Another situation could be that they talk to him in a very patronizing tone, as if he doesn't understand anything. Maybe they try to feed him or dress him as if he were incapable of doing these basic things himself.
His relationships would likely be very different. Those who were once his equals or even subordinates might start to look at him in a new light. They could either try to dominate him as one would an animal or become overly protective. Naruto's usual boisterous and confident self would be overshadowed, and he'd have to adapt to this new view others have of him, which could strain or strengthen his bonds depending on the character.
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.
A popular plotline is Naruto going on solo adventures. He feels neglected by Team 7, so he decides to prove himself on his own. He takes on dangerous missions alone, meets new characters, and discovers hidden powers or secrets. This not only shows his independence but also his determination to not let the neglect hold him back.
One common plotline is the corruption arc. Naruto starts off on his normal path but then gradually gets influenced by Orochimaru - like ideas of power. For instance, he might be tempted by the idea of using forbidden jutsu to gain an edge in battles, similar to how Orochimaru was always seeking new and powerful techniques through unethical means.
One common plotline could be Naruto leaving his family behind and finding a new family in his friends. For example, he might feel so estranged from his blood relatives that he decides to build a closer bond with Sasuke, Sakura, and Kakashi, seeing them as his true family. Another plotline could involve Naruto trying to discover the reasons behind his hatred. Maybe he uncovers some long - hidden family secrets that made him develop such strong negative feelings.
Some fanfictions explore the idea of Naruto being betrayed by a new character introduced into the story. This new character could be secretly working for an enemy and manages to turn Naruto's closest allies against him by using their insecurities. This creates a complex web of relationships where Naruto has to fight not only the external threats but also the internal ones within his group.