One possible reason could be the burden of his past. Naruto has faced a lot of hardships and the memories might be overwhelming him, making him want to be alone. For example, the loss of his master Jiraiya might have left a deep scar, and he might feel that isolating himself is the only way to deal with that pain.
Maybe he feels a sense of guilt. For example, if something bad happened in the village that he blames himself for, even if it wasn't really his fault. He could exile himself as a form of self - punishment. He has always been very hard on himself when it comes to the well - being of the village and his friends.
Well, while there might be some out - of - character fanfictions out there, the general perception of Naruto is that he is a very selfless character. His whole journey in the original story is about protecting others and achieving peace for everyone. So, in fanfiction, it's not very common for him to be portrayed as only caring for himself. Usually, the essence of his character is maintained, which is his altruism.
In some fanfictions, Naruto might distance himself because he discovers some dark secrets about the ninja world or his own past. These revelations could shock him so much that he needs time alone to process and figure out how to deal with them.
Perhaps in the fanfiction, Naruto discovers some dark secrets about his past, like his family's involvement in something he considers immoral. This new knowledge could make him question his own identity and lead to self - hatred. He might feel that he's a product of something bad and that he can't escape this 'taint' no matter how hard he tries.
In fanfiction, Naruto sacrificing himself for Obito could be a very emotional and dramatic concept. It might show Naruto's ultimate selflessness, believing that Obito is worth saving at the cost of his own life. This could be due to Naruto seeing the good in Obito that others might not, like the part of Obito that was once a kind - hearted shinobi.
In many Naruto fanfictions, Naruto might push himself by over - training. He could be constantly trying to master new jutsus at a faster pace. For example, he might practice a new Rasengan variation until he's completely exhausted, not giving himself a break. He may also push himself in terms of physical endurance, like running long distances with heavy weights.
In some versions of fanfiction, Naruto might use a new and powerful sealing jutsu that he has either created or learned specifically for this purpose. It could be a jutsu that combines his Uzumaki heritage's sealing knowledge with his own unique chakra control.
Jiraiya could still play a role. Even if Naruto is raising himself, Jiraiya might cross paths with him and see his potential. He could offer some sporadic guidance without fully taking Naruto under his wing.