Naruto might be really confused at first. He's used to people being friendly or having normal crushes, but a yandere is a whole different level. He'd probably try to talk to her and understand why she's acting so strangely.
Naruto might also feel a sense of responsibility. He might think that he did something to cause Yugito to act this way. So he could start to limit his own actions to avoid triggering her yandere behavior. For instance, he might stop being so friendly with other girls in front of her. But at the same time, he would not give up his own dreams and values, and would try to make Yugito understand that her behavior is not acceptable in a way that is both firm and kind.
At first, Naruto might be really confused. He's used to the normal Sakura, so when she starts acting all yandere, he'd be like 'What's going on, Sakura - chan?'. He'd probably try to talk to her and find out what's wrong.
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.
In a fanfiction, Naruto could be training in a secluded area and Yandere Koneko stumbles upon him. She immediately falls for his spunk and the fact that he doesn't give up easily. Yandere Koneko then tries to insert herself into Naruto's life by bringing him food and small gifts. Naruto is initially confused but then realizes she has a rather extreme way of showing affection and has to gently set boundaries.
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.
A more complex fanfiction could involve Yandere Chan being a part of an experiment by Orochimaru. He combines some of her yandere traits with ninja abilities. She then targets Naruto, believing he has some special power that she needs. Naruto has to not only deal with her attacks but also try to understand her motives and perhaps find a way to reverse Orochimaru's experiment on her.
One common theme is possessiveness. The yandere characters in these fanfictions often show extreme possessiveness over Naruto or other characters. For example, they might not allow the object of their affection to be around other people.
Sakura's yandere nature can make the plot full of drama. For example, if Naruto is supposed to go on a mission with another teammate, Sakura might try to stop it out of jealousy. This creates conflict right away. It can also lead to unexpected twists. Maybe Sakura will frame someone who she thinks is getting too close to Naruto, and Naruto has to figure out the truth while still dealing with Sakura's erratic behavior.
Well, at first, Naruto might be oblivious to Hinata's yandere tendencies. But as they start to surface, it can create a lot of confusion. Hinata's extreme love and possessiveness could make Naruto question her true nature. He might start to pull away from her, which in turn would make Hinata even more desperate to keep him close. It could turn into a cycle of her being overly clingy and Naruto trying to regain his freedom, ultimately affecting the trust and closeness they once had.