Well, it could be a secret organization that has been operating in the shadows. They might have some ulterior motive related to Naruto's power or his connection to the Nine - Tails. Maybe they believe that by kidnapping Naruto, they can control the Nine - Tails and use it for their own purposes. Another option is a jealous ninja from within Konoha. This ninja might feel overshadowed by Naruto's achievements and popularity and decides to kidnap him to get him out of the picture. Also, a powerful and ancient being awakened from a long slumber could be the kidnapper. They see Naruto as a source of energy or a key to something they desire.
It could be Orochimaru. He has always been interested in Naruto's power and potential. He might kidnap Naruto to try and extract the Nine - Tails' chakra or study his unique Uzumaki bloodline further. Another possibility is a group of rogue ninjas who want to sell Naruto to the highest bidder, thinking his value as a Jinchuriki would make them rich.
One possible storyline could be that Naruto is kidnapped by a rogue ninja group who wants to use his power for their own evil deeds. They might try to force him to reveal the secrets of his special jutsu. Another could be that he is kidnapped by a mysterious organization that believes he is the key to a long - lost prophecy. They hold him captive while they try to figure out how to use him to fulfill the prophecy. A third storyline could be that Naruto is kidnapped by a group of enemy ninjas from another village who see him as a threat to their plans for domination.
One common trope could be the rescue mission. After Naruto is kidnapped and tortured, his friends or allies would likely embark on a dangerous rescue mission. Another might be the transformation of Naruto's character. The torture could potentially lead to him becoming more jaded or having a new perspective on life. Also, there could be the trope of the villain's motives. The kidnapper might have some convoluted reason for targeting Naruto, like trying to gain power through his unique abilities or to send a message to the Hidden Leaf Village.
One possible motive could be power. If Naruto has some unique abilities or is a key to something powerful in the fanfic world, the kidnappers might want to control him to gain that power for themselves.
He could use his ninja skills. Naruto is a highly skilled ninja. He might find a moment of weakness in his captors' defenses and use his combat abilities, like his Rasengan or Shadow Clone Jutsu, to break free.
A plot like Naruto being kidnapped and tortured in a fanfic can really divide the fandom. On one hand, it might attract those who are interested in exploring the psychological and emotional depths that such a situation could bring out in the character. But on the other hand, many traditional fans who are used to the more heroic and upbeat Naruto stories might find it too much to handle. It also might make new fans who stumble upon it have a warped view of what the Naruto franchise is really about.
One possible plot twist could be that the kidnappers are actually being controlled by an old enemy of Naruto's village who wants to use him as a bargaining chip to get some ancient scrolls. Another could be that Naruto is kidnapped by someone who thinks he is the key to a powerful jutsu they want to unlock, but in reality, they have the wrong idea about Naruto's abilities. Maybe the kidnappers are from a hidden group within the ninja world that has a grudge against the Uzumaki clan and Naruto specifically.
Naruto might be initially confused. He trusts Tsunade, so being kidnapped by her would be completely unexpected. He would probably start by asking her why she's doing this.
They might find an ally within the place where they are held. There could be another being there, maybe an angel who doesn't agree with Castiel's actions, or a human who has also been captured by Castiel in the past and knows the layout well. Together, they could come up with an escape plan.