Well, in some fanfictions of this kind, Naruto could be tortured physically by being chained up and beaten. His captors might also starve him or deprive him of water to weaken him. It could also be that they use some sort of dark magic or forbidden techniques on him that cause extreme pain and discomfort.
In 'naruto gets tortured fanfiction', there could be a scenario where Naruto is tortured by a group of rogue ninjas. They might use poison on him that slowly eats away at his chakra and causes him great pain. They could also try to break his spirit by constantly taunting him about his past failures and how he'll never be able to protect his village. This would not only be a physical but also a mental torture for Naruto.
One possible scenario could be that he is captured by an enemy ninja group who wants to extract information from him. They might use various cruel methods like chakra - draining techniques or physical harm. Another could be that he is tortured as a form of revenge by someone he has defeated in the past.
In 'naruto gets angry fanfiction', one possible scenario could be that Naruto gets angry when he discovers someone has been mistreating his friends in the village. He might immediately confront the wrongdoer with his signature rasengan at the ready.
Well, in 'naruto gets stabbed fanfiction', it could be that Naruto is exploring a new and dangerous area where he encounters a powerful and hostile ninja. In the heat of the fight, this ninja manages to land a stabbing blow. It might also be that Naruto is weakened due to some prior injury or chakra depletion, making him more vulnerable to being stabbed by a regular enemy. And, there could be a situation where Naruto is under the influence of some sort of genjutsu that impairs his ability to defend himself and thus gets stabbed.
In a 'naruto gets bullied fanfiction', perhaps Naruto is bullied by the children of the more respected ninja clans. They could use their family's status to intimidate him and make him feel inferior. They might also spread false rumors about him, which further isolates Naruto from the rest of the village.
One possible scenario could be that Naruto gets pissed off when he discovers someone has been spreading false rumors about his friends in the fanfiction. This would really push his buttons as he values his friends highly.
One possible scenario could be that Naruto is constantly taunted in the streets. The villagers might throw things at him or call him mean names, like 'demon brat'. Another could be that they exclude him from village activities, making him feel like an outcast.
Perhaps Gaea uses Percy's own insecurities against him in this fanfiction. She might dig into his fears about not being able to protect his friends and family. By constantly whispering these fears in his mind, she could mentally torture him. This could be combined with physical torture, like having him trapped in a dark, claustrophobic space underground, which would heighten his sense of helplessness.
One possible scenario could be a power imbalance. Maybe Sasuke discovers some new, extremely powerful jutsu that Naruto has no defense against. For example, a jutsu that can nullify Naruto's chakra or attack his spirit directly. Another possibility is a miscommunication or a breakdown in their relationship. If Sasuke believes Naruto has betrayed him in some way, his anger could lead him to kill Naruto. However, this goes against the core of their bond in the original series.
In the 'naruto gets chakra chains fanfiction', perhaps Naruto discovers that the chakra chains can be used to connect with other people's chakras in a positive way. For example, he could use them to heal his friends or share his chakra more efficiently. Also, it could be that the chakra chains are a sign of a new power level for Naruto, which makes him a more formidable opponent against stronger enemies.
Sometimes, it's just a way to shock the audience. Fanfiction authors often like to take risks and do unexpected things to their beloved characters. Torturing Natsu can be a very unexpected and extreme move that can leave a lasting impression on the readers, whether they like it or not.