One plotline could be that his sister is being controlled by an enemy. Naruto has to fight her to break the control. He uses his Nine - Tails chakra to overpower her and then uses his talk - no - jutsu to bring her back to her senses, thus defeating her in a sense.
In the Naruto series, Naruto doesn't have a biological sister in the original story. So in this fanfiction, the author probably creates a new character to be his sister. It could be an original character with unique abilities and a complex backstory that leads to the situation where Naruto dies by her hand.
She could be an original character created specifically for this fanfiction. The author might give her unique abilities and a distinct personality to make the story more interesting.
One possible reason could be to protect her. Naruto might believe that by leaving, he can draw danger away from his sister. For example, if there are powerful enemies targeting him, he doesn't want his sister to get caught in the crossfire.
The relationship could start with Naruto being overly protective of his sister, but she wants more independence. This causes friction. Later, when she gets into trouble that only Naruto can help her with, he steps in. This makes her realize that his over - protectiveness comes from love, and they begin to repair their relationship. For instance, if she is kidnapped by a powerful enemy, Naruto uses all his skills to rescue her, and during this process, they have heart - to - heart conversations.
One idea could be that their own village betrays them. Maybe there's a power - hungry leader who sees Naruto and his sister as threats to their new regime. They could be framed for a crime they didn't commit and then forced to flee the village. In the process, they might have to rely on some unlikely allies they meet on their journey, like a group of outcasts who also have a grudge against the village.
In some fanfictions, Naruto might defeat Zabuza through new jutsu. For example, he could develop a unique shadow clone variation that overwhelms Zabuza's water jutsu. Maybe he combines his Rasengan with some unexpected element, like wind chakra in a new way that Zabuza can't counter.
One common element is Naruto's growth. He usually has to reach a new level of power or understanding to defeat Madara. For example, he might gain a new jutsu or a deeper connection with his inner chakra.
Another possibility is that Naruto could defeat Kakashi if the latter was in a weakened state. Maybe Kakashi had just come out of a tough battle with other powerful enemies and was low on chakra. Meanwhile, Naruto was at his peak, full of energy and ready to fight. In this situation, Naruto's sheer determination and his own strong abilities could lead to his victory.
In a more psychological approach, Naruto could have grown so much as a character that he no longer fears Kakashi's reputation. This new - found confidence could change the dynamics of their fight. He might be able to read Kakashi's moves better and anticipate his attacks. Combined with his own ever - improving skills, Naruto could defeat Kakashi in this state of mental superiority.