The story might focus on how Fem Harry, as Naruto's sister, would change the existing relationships in the Naruto universe. For example, she could have an impact on Sasuke. Maybe she'd see the similarities between Sasuke's situation and some of the characters in the Harry Potter world who were on a path of revenge. And she could use her own experiences to try and turn him away from the dark side. Also, her presence could affect the way the ninja villages interact, as she has a different cultural background from the world of ninjas.
Well, the plot could involve her adapting to the ninja world. Maybe she'd bring some of her magic knowledge from the Harry Potter universe, like using spells in a new way to mimic ninja techniques. She could also have a special bond with Naruto, being his sister, and help him in his journey to become Hokage, like using her intelligence to outwit enemies.