I'm not sure specifically which ones are the most popular. However, in general, these types of fanfictions might explore dark themes such as Naruto being wrongly accused and then facing various forms of torture. They often deviate from the original positive and heroic narrative of the Naruto series.
There could be many out there. Some might involve Naruto being framed by his enemies within the Hidden Leaf Village. For example, they could set him up to look like he's committed a serious crime against the village. Then, the torture part could be physical, like being put in a prison with harsh conditions, or mental, such as being isolated and having his friends turn against him because of the false accusations.
Honestly, it's a rather dark and niche area of fanfiction. One possible scenario in these fanfictions could be that Naruto is framed by a powerful and shadowy organization within the Naruto universe. They manage to manipulate evidence to make it seem like he's a threat. As for the torture, it could be in the form of being experimented on with some sort of forbidden jutsu, which is a very different take from the usual Naruto story where he's the hero saving the day.
Chapter 281, ", Torn to Pieces", is the clearest early answer because it turns Anat's situation into a concrete plot event. The setup is Irong Fetches would never be caught 'off guard'., but the pressure keeps building through But even the process of visual system detection, logical calculation,....
Chapter 437, ", Humanity Will Prevail", is the clearest early answer because it turns Green Skins's situation into a concrete plot event. The setup is They're bearable when the wind is in their sails; they can even be..., but the pressure keeps building through But let a little adversity blow their way, and you'll see those....
Chapter 429, ", Battle Moon", is the clearest early answer because the buildup finally cashes out in a real clash. The chapter turns that into something concrete by moving from After the Mechanical Sect Fleet had departed, Wu Jiarong herself was... to Hope for victory was near, and naturally, they were happy.. What makes it stick is that the danger stops being abstract and the conflict around Battle Group becomes immediate, forcing the surrounding cast to react under pressure.
Chapter 405, ", The Defector Interstellar Warrior", is the clearest early answer because the buildup finally cashes out in a real clash. Early on, Over time, the Pirate Group went so far as to directly recruit.... By the end, The key point was, he wasn't a pirate, and his planet couldn't move.. Inside the broader faction conflict storyline, the danger stops being abstract and the conflict around technology upgrade becomes immediate, forcing the surrounding cast to react under pressure.
Chapter 439, ", Temir No.5 Meat Grinder", is the clearest early answer because it turns Green Skins's situation into a concrete plot event. The chapter turns that into something concrete by moving from The war situation on Temir No.4 was progressing basically as planned... to It was alright during defense, but during offense, the caverns were....
Chapter 433, ", Subversion Operation", is the clearest early answer because it turns Demon Hunters's situation into a concrete plot event. A useful checkpoint is the way the scene starts with Pushing open the door to the innermost room on the ground floor of... and follows through with However, after learning about Arno Chinko's plan to unite the power....
Chapter 346, ", We Will Not Fail Our Mission!", is the clearest early answer because it turns Gu Hang's situation into a concrete plot event. The setup is Gu Hang gently patted his mother's hand, signaling her to be at ease,..., but the pressure keeps building through Those who had recovered from the initial shock of his declaration....
Chapter 363, ", Something is Wrong", is the clearest early answer because it turns Primal Fury Owl's situation into a concrete plot event. The chapter gives readers a real answer by opening on At this moment, Gu Hang was on the verge of losing consciousness. and ending on The only power he could employ was his own..
Chapter 299, ", Truly Tough Fate", is the clearest early answer because it turns Mechanical Cult Guild's situation into a concrete plot event. It opens with Gu Hang wasn't at all embarrassed, "If you want to talk, I'll keep... and closes on Reporting upwards that they had produced an A-level spiritual energy.... The key payoff is that the chapter closes with Gu Hang was nothing if not accommodating: "Okay, Master Wang, we can talk later.
Chapter 437, ", Humanity Must Triumph", is the clearest early answer because it turns Marshal Zhu's situation into a concrete plot event. The chapter turns that into something concrete by moving from Among them were warriors, heroes, and even women and children. to I'll go find someone to write this up, to boost morale!. What makes it stick is that the chapter closes with Owe 64k, which gives Marshal Zhu a stronger narrative position and pushes the power growth onward.