Start with a strong inciting incident. For example, Kaguya could be resurrected with a yandere - like obsession for Naruto due to some dark magic. Then, build up the conflict as Naruto tries to resist her advances while also dealing with the chaos she causes in the ninja world.
You could develop the plot by having Kaguya manipulate events behind the scenes to get closer to Naruto. As the story progresses, Naruto could start to notice the strange occurrences and suspect Kaguya. This would lead to a cat - and - mouse game between them, with Naruto trying to expose and stop her while she becomes more and more determined to make Naruto hers. Along the way, other characters could get involved, adding more complexity to the plot.
Their relationship might start with Kaguya being instantly drawn to Naruto because of his strength and positive energy. But as her yandere side kicks in, she becomes over - possessive. Naruto would be confused at first, but gradually try to understand her.
One idea could be that Naruto somehow gets trapped in a dimension where Kaguya has become a yandere for him. She tries to keep him there all to herself, while Naruto has to figure out a way to escape and also deal with her obsessive behavior.
Well, a possible plot could be set in an alternate universe where Kaguya is resurrected as a yandere. She sees Naruto as the key to her new world order and her yandere love makes her go to extreme lengths to get him on her side. Maybe she uses her powers to create illusions that only Naruto can see, trying to manipulate his perception of reality and draw him closer to her.
At first, it might be one of suspicion. Naruto would be wary of Kaguya's power and her past as a sort of villain. But as they face challenges together, they could start to respect each other. Naruto might see the good in Kaguya that was buried under her past actions, and Kaguya could come to admire Naruto's tenacity and his strong sense of justice.
The plot could start with the other characters being oblivious to her yandere nature. As the story progresses, her actions would start to raise suspicions. For example, if there's a training session and she gets overly aggressive towards someone who accidentally hurt her love interest during sparring.
Often, it starts with the yandere character becoming infatuated with Naruto. They might start by observing him from afar and then gradually insert themselves into his life. Their actions are driven by their extreme love which can border on possessiveness.
His understanding of the ninja world would expand. He might become more cautious and calculating in battles, as Kaguya's training could expose him to different strategies. Also, he could develop a more solemn side to his personality, considering Kaguya's own complex nature and the heavy knowledge she might share.
Their relationship could develop realistically if Naruto starts by seeing the pain in Kaguya's past. He has a history of empathizing with his enemies, like Nagato. So, he could begin to understand why Kaguya did what she did. This understanding could be the first step in them forming a connection.
There are fanfictions where Kaguya and Naruto are forced to work together due to some external threat. At first, they clash because of their different views and powers. However, as they face challenges side by side, they come to realize that they have more in common than they thought. This realization deepens their relationship, and they might even become friends or allies in the long run, with Kaguya perhaps having a change of heart about her previous destructive ways.
The story could develop with the ninja world exploring new forms of ninjutsu or chakra control now that Kaguya's influence is no more. For example, they might discover new ways to harness natural energy without the fear of it being corrupted by Kaguya's power.