In such a fanfiction, the plot could be centered around a misunderstanding. Maybe Naruto's sister has been influenced by a villain who has made her believe false things about Naruto or the village. Naruto, being the hero he is, would initially try to talk to her but when she attacks, he has no choice but to fight back. It could also be a test of Naruto's growth, as his sister might be extremely powerful and he has to use all his skills and newfound powers to face her.
Perhaps Naruto's sister is jealous of the attention Naruto gets as the hero of the village. This jealousy festers and turns into hatred. One day, she challenges Naruto to a fight. Naruto is confused and hurt but has to defend himself. The fight could be a display of different jutsus. Naruto might hold back at first, still hoping to resolve things peacefully, but as the fight progresses, he realizes he has to be more serious to stop her from causing more harm.
One possible plot is that Naruto's brother is jealous of Naruto's status as a hero. He decides to challenge Naruto to prove himself. The fight might start with some basic exchanges of punches and kicks. But as it progresses, they both start using their more advanced ninja skills. Naruto may struggle because he doesn't want to hurt his brother too much, but he also knows he has to stop his brother's dangerous actions.
One possible plot could be that Naruto is mislead into believing his family has been possessed by some dark force. So, he has to fight them to free them. For example, an evil ninja might use a genjutsu on his family members, making them act against Naruto's will.
In this fanfiction, perhaps Naruto's sister has some special power. Naruto loves her not only because she's family but also because he sees the good in her power. He might teach her how to control it and use it for good. They could go on adventures together, with Naruto always being the over - protective brother and making sure she doesn't get into too much trouble.
Perhaps in this fanfiction, his sister has done something wrong or dangerous, and Naruto has to 'beat' her in the sense of stopping her. It could involve a moral or ethical conflict within the story that Naruto has to resolve by overpowering his sister's actions.
Well, it could be about Naruto and his sister having different loyalties. Say, Naruto is loyal to the village, but his sister has a connection to an outside group that Naruto doesn't trust at first. They end up in a conflict until they realize they can work together to achieve a greater good for both the village and the outside group's worthy cause.
Well, one possibility could be that Naruto is initially shocked to discover he has a sister. Maybe she was hidden away for some reason, like to protect her from the same threats Naruto faced as a Jinchuriki. They might bond over their shared family history and Naruto could finally have a real family connection that he always secretly longed for.
In a 'naruto fights alone fanfiction', it could be that Naruto is on a mission in a foreign land where he has no support. The local ninjas are all against him for some reason. He has to use his Nine - Tails chakra in a more discreet way as he can't afford to go all - out and draw too much attention. He might befriend some local animals or spirits who help him in a more indirect way, like giving him information about the enemies' weaknesses.
Well, one possibility could be that Naruto uses his shadow clone jutsu to confuse the Humunculi. Since they are used to a more straightforward combat style, the clones might throw them off. Naruto could then use his Rasengan to directly attack them. Maybe he would also team up with some of the characters from the FMA world who oppose the Humunculi.
One possible plot could be that Zeref has a new target in the Naruto universe. Naruto discovers this and decides to confront him. At first, Naruto is outmatched as he doesn't understand Zeref's magic. But then he starts to analyze it during their battles and figures out ways to counter it. Meanwhile, Zeref is intrigued by Naruto's never - say - die attitude and chakra. The plot could also involve other characters from both universes getting involved, either to help or to cause more chaos.
Well, the plot could involve Naruto being in a post - apocalyptic world filled with zombies. His ninja skills would be put to the extreme test. He could team up with his friends like Sasuke and Sakura. Naruto would have to adapt his fighting style as zombies don't feel pain like normal foes. He might use his speed and agility to dodge the zombies and then use his powerful ninjutsu to take them out in groups.