Naruto might initially be shocked and angry. He has a strong sense of justice and being kidnapped goes against everything he stands for. He would likely try to fight back immediately, using his basic ninja skills and his determination. For example, he could try to use his Shadow Clone Jutsu to create distractions and escape.
Well, in this fanfiction, perhaps Itachi is being manipulated by some dark force. He kidnaps fem Naruto because he's under the control of this force which thinks that Naruto, being female in this version, holds the key to some sort of ancient prophecy. Itachi is then in a struggle between his loyalty to the village and the commands of this dark entity.
Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
Well, in such a fanfiction, Itachi might kidnap Hinata for various reasons. Maybe he's being controlled by some dark force and needs Hinata for some ritual. Or perhaps he's been misinformed that Hinata has some special power that can help him in his secret mission against the Hidden Leaf Village.
Well, one possibility could be that Itachi has some hidden motive related to the Uchiha clan's secrets. He might think Kakashi knows something crucial. So, he kidnaps him to interrogate him in a secret location.
It could be that Itachi is being controlled by some dark force or an enemy. He doesn't really want to harm Sakura but has no choice. The fanfic might then focus on Sakura trying to figure out how to break the control on Itachi while also trying to escape from the situation. She could use her medical ninjutsu skills to her advantage in some way.
Itachi himself could be seen as the main antagonist in this scenario as he is the one carrying out the kidnapping. He is acting against Sakura's will and causing a dangerous situation for her.
Well, one possibility is that Itachi has some hidden motives. Maybe he believes Sakura has knowledge about something important in the ninja world, like a secret jutsu or information about an enemy. So he kidnaps her to extract that information.
In such a fanfic, perhaps Itachi kidnaps Sakura for some strategic reason related to the shinobi world. Maybe he thinks Sakura has some knowledge or ability that could be useful to his goals. For example, her medical skills could be crucial for treating someone in his group.