One possible motive could be to force Naruto to understand his own power. Sasuke might think that by kidnapping Naruto, he can push Naruto to a situation where he has to tap into his full potential. Maybe Sasuke feels that Naruto has been relying too much on his friends and needs this shock to grow stronger on his own.
Another reason could be related to Sasuke's own inner turmoil. He might be confused about his feelings towards Naruto. By kidnapping him, he can have Naruto all to himself, away from the distractions of the village and their friends. It could be a very complex and mixed - up emotional drive, where Sasuke doesn't really know what he wants but feels compelled to take Naruto.
One possible motive could be related to power. Maybe Sasuke thinks that Hinata has some sort of connection or knowledge that could help him gain more power. For example, her Byakugan might be of interest to him in terms of seeing things that he couldn't otherwise. Another motive could be a misdirected sense of revenge. He might believe that Hinata is somehow connected to someone he wants to get back at. It could also be a plot by an outside force that is controlling Sasuke to kidnap Hinata, perhaps for some kind of experiment due to her unique abilities.
It could also be a matter of desperation. Perhaps there is a threat to the village or someone she loves dearly, and she believes that Naruto holds the key to solving the problem. But instead of asking him directly, she kidnaps him in a hasty and ill - conceived plan. This could lead to a lot of drama and character development as Naruto tries to understand her actions and they both work towards resolving the real issue.
Well, in this kind of fanfiction concept, it could be a very interesting plot twist. Naruto, being female, might have some strong motives for kidnapping Sasuke. Maybe she believes she can protect him better this way from the various threats in the Naruto world. It could also lead to a different kind of relationship development between them, far from the traditional friendship or rivalry.
Maybe she's trying to protect Naruto from something she knows about but others don't. She might think that by kidnapping him, she can keep him safe from an imminent threat that the village or his friends are unaware of.
It might be for Naruto's own good. Sasuke may believe that Naruto is on a dangerous path that will lead to his downfall. So he captures him to keep him from making bad decisions, like sacrificing himself for the village or something similar. He wants to save Naruto from himself in a sense.
One possible motive could be love. In the fanfiction, female Naruto might be secretly in love with Sasuke and sees kidnapping as a way to keep him close. Another motive could be to prevent Sasuke from seeking revenge. She may think that by kidnapping him, she can stop him from going down a dark path that will lead to his destruction.
It could be that Naruto has lost his sanity temporarily. The stress of being a hero, the constant battles, and the losses he has endured might have taken a toll on his mental state. In this state of instability, he may see Sakura as a symbol of something he wants to preserve or protect, but his way of doing so is through kidnapping. Or there could be a new villain in the story who has the ability to make Naruto act out of character, and this villain's plan involves Naruto kidnapping Sakura.
Naruto would probably be very confused at first. He trusts Sasuke, even if it's a Fem Sasuke in this fanfiction, and he wouldn't expect to be kidnapped by her. So, his initial reaction might be to try and talk to her, asking her why she's doing this.
Naruto could use her shadow clone jutsu. She could create multiple clones while Sasuke is distracted and then make her escape. Since she has a large amount of chakra, she can afford to create a lot of clones to confuse Sasuke.
The Hidden Leaf Village would surely launch a rescue mission. This would involve characters like Kakashi, Sakura, and the other ninja. Their efforts to find Naruto would be a major part of the story. Meanwhile, Sasuke might be moving Naruto from one location to another to avoid being caught, which would add more twists and turns to the plot.