The plot could involve Naruto delving into the history of his family and Kaguya's past. He could learn secrets that were long buried, and this knowledge could be used to either save the ninja world from a new threat or to bridge the gap between different ninja clans that have been at odds because of Kaguya's actions in the past. Naruto's new status as Kaguya's brother could be a catalyst for great change in the Naruto universe.
Well, it could be that Naruto is in a near - death situation, poisoned or severely injured. Kaguya, having a change of heart, decides to save him. She might use her chakra to heal Naruto's wounds and restore his strength. It could also be that Kaguya saves Naruto from a trap set by an ancient evil that she has knowledge of. She steps in because she realizes Naruto's importance in the balance of the ninja world.
One possible plot could be that Naruto, in his godlike state, tries to understand Kaguya's past and motives more deeply. He might use his newfound power to communicate with her on a different level, perhaps even showing her a different way of seeing the world. This could lead to a redemption arc for Kaguya, where she starts to regret her past actions.
In this fanfiction, perhaps Naruto breaks Kaguya by outsmarting her. He could use his quick thinking and knowledge of her weaknesses. He might form alliances with other characters in ways that give him an edge over Kaguya, and then use his signature Rasengan in a new and unexpected way to break her power.
The plot could also involve Naruto raising Kaguya to be a force for good in a world that still has remnants of evil. Kaguya, with Naruto's guidance, could use her vast power to help in rebuilding areas damaged by past wars. Naruto may also introduce her to the concept of family, which she may have lost touch with long ago, and this new understanding could transform her character completely.
The plot might involve Naruto learning about his heritage as Kaguya's son. This could lead to a whole new understanding of the ninja world for him. He might face discrimination from some who fear his power, while others see him as a potential savior. He could also have to unlock the secrets of Kaguya's power within himself to face a great threat.
One possible plot could be that Kaguya is somehow revived in a different form. Naruto, being the one who always tries to understand his enemies, starts to communicate with her. Through their interactions, they gradually develop feelings for each other. Maybe Kaguya sees in Naruto the hope and kindness that was lacking in her own life before.
One possible plot could be that Naruto, under Kaguya's training, gains godlike powers at an accelerated rate. He might learn ancient and powerful jutsu that were once exclusive to Kaguya. This could lead to him facing new and extremely powerful enemies, perhaps even threats from other dimensions. With Kaguya's guidance, Naruto could also gain a deeper understanding of the chakra and its origins, and use this knowledge to reshape the ninja world for the better.
One possible plot could be that the fused character has a unique power set. Since Naruto has his various jutsus like Rasengan and shadow clones, and Kaguya has her all - powerful abilities. The fused fem Naruto - Kaguya might use these powers to protect the ninja world from a new, greater threat that neither Naruto nor Kaguya could have faced alone. For example, a group of rogue ninja who have found a way to nullify the most common jutsus in the ninja world. The fused character's unique perspective, a blend of Naruto's determination and Kaguya's ancient wisdom, could lead to new ways of fighting and protecting the land.
The fanfiction might involve Naruto having some sort of encounter with Kaguya in a different dimension. This encounter could lead to a series of events where Naruto has to either team up with Kaguya against a new common enemy or try to prevent her from doing something bad again. Since Kaguya was a very powerful and complex character, the fanfiction could explore many different aspects of her power and how Naruto would deal with it. For example, Naruto could learn new jutsu or abilities from Kaguya or find a way to seal her power in a different way. Also, it could be a story about Naruto's journey to redeem Kaguya, believing that there was some good in her despite all the bad things she had done.
One possible plot could be that Kaguya is somehow resurrected in a different form or time. Naruto, being the hero, encounters her and instead of fighting, they develop an understanding. Over time, this understanding turns into love and they get married. They could then face challenges together, like threats from old enemies who don't approve of their union or dealing with the power imbalance between them.