How about a plot where the female Naruto discovers a hidden part of her family history that gives her access to a special type of ninjutsu. However, there are those who want to stop her from learning this ninjutsu because they fear she will become too powerful. So she has to fight against these opponents while also trying to master this new power and prove that she will use it for good.
A great plot could involve the female Naruto being sent on a diplomatic mission to another village. There, she discovers a conspiracy against the Hidden Leaf Village and has to use her wits and ninja skills to expose it and prevent a war. Along the way, she also forms unexpected friendships with some of the villagers from the other village, which helps her in her mission.
Perhaps in the fanfiction, the female Kurama forms a special bond with Naruto where she can transfer some of her unique powers to him in a different way than in the original story. This could lead to Naruto developing new jutsu and facing new enemies that are attracted by this new power. For example, a group of rogue ninjas who want to steal this power-transferring ability.
One idea could be a female Naruto who has a special ability related to healing. She could use this to not only heal her friends in the Hidden Leaf Village but also to try and bridge the gap between different ninja clans. For example, she might use her healing powers to save a member of a rival clan during a battle, which would then lead to a series of events where the two clans start to cooperate more.
A possible plot could involve Female Itachi being an outcast in her own clan because she has different ideals. Naruto, who always believes in people, befriends her. They then start a journey to prove that her ideas can bring peace to the ninja world, facing opposition from both their own and other clans.
A plot could be that Female Naruto and Choji enter a cooking competition in the village. Since Choji loves food, he could be the main cook while Naruto helps with gathering ingredients. Along the way, they face some sabotage from other competitors who are jealous of their teamwork.
Maybe in this fanfiction, Naruto as a female could develop a different kind of relationship with Sasuke. Since the dynamic between male - female friends can be distinct from male - male friendships, it could lead to new story arcs and character growth for both of them.
Maybe the female cell comes from an ancient and powerful clan. Naruto has to figure out how to control this new power within him without being consumed by it. He could go on a journey to learn more about the origin of the cell and in the process, meet new characters related to that clan.
Perhaps a plot where the female Kyuubi has to take on a human form to protect Naruto from a new, powerful enemy. In the process, they develop feelings for each other while fighting side by side.
Well, for a Naruto and female shinigami fanfiction, a plot could involve a female shinigami who is an outcast in her own realm because she believes in a different way of handling souls. She crosses into the Naruto universe and meets Naruto. They bond over their shared experiences of being different. Naruto could learn about the afterlife and the concept of souls from her. And she could learn about chakra and the ninja way. Also, perhaps there's a dark force in the Naruto world that is related to a corrupted form of soul - handling, and the female shinigami's knowledge helps Naruto combat it.
One idea could be that female Haku, with her unique ice - related abilities, teams up with Naruto on a special mission in a frozen land. They have to rely on each other to survive and complete the mission, which leads to a deepening of their friendship.
One plot idea could be that Female Gaara, being the Kazekage, forms an alliance with Konoha led by Naruto. They start off as cautious allies but gradually develop a deep friendship as they face common threats. Their different leadership styles - Gaara's more reserved and Naruto's more exuberant - could create interesting dynamics.