It's popular because it shows a different side of Naruto. We usually see him with his friends, but when he's all alone, it creates a sense of vulnerability that's really interesting to explore.
One could be 'Naruto's Solitary Journey'. In this fic, Naruto is left alone after a major battle where most of his friends are thought to be dead. He embarks on a journey of self - discovery and revenge. Another might be 'Alone in the Shadows', where Naruto is ostracized by the village again and has to face new threats all by himself.
One interesting 'naruto all alone fanfiction' story could be about Naruto finding himself alone in a desolate forest, having to rely on his own skills and inner strength to survive. He might encounter strange creatures and have to figure out how to deal with them without his usual comrades.
First, focus on Naruto's character. Since he's alone, you can explore his internal thoughts more deeply. For example, his insecurities that he might not show when he's with his friends. Second, create a unique setting for his isolation. It could be a mysterious island or an abandoned village. Third, think about the challenges he'll face. They should be different from the ones he usually faces in the main series because he doesn't have his friends to rely on. This will make the fanfiction more interesting.
One common theme is self - discovery. When Naruto is alone, he often has time to think about who he is and what he wants. Another theme is inner strength. He has to rely on his own abilities and not depend on others. For example, in many fanfictions, he overcomes great difficulties alone using his own skills.
He could meet an old enemy who has also changed after the war. This enemy might now be in a similar situation of being alone and they could form an unexpected bond as they understand each other's isolation.
He might meet an old sage who has been living in seclusion near the village. The sage could see Naruto's loneliness on his birthday and offer him some ancient ninja knowledge.
Maybe an ancient evil ninja who was sealed away long ago but has now been released. This antagonist could have powers that nullify any communication or summoning jutsu, forcing Naruto to fight alone. He would be extremely powerful and know many forgotten and deadly jutsu.
In a 'naruto fights alone fanfiction', it could be that Naruto is on a mission in a foreign land where he has no support. The local ninjas are all against him for some reason. He has to use his Nine - Tails chakra in a more discreet way as he can't afford to go all - out and draw too much attention. He might befriend some local animals or spirits who help him in a more indirect way, like giving him information about the enemies' weaknesses.