One reason could be the shock of the revelation. Harry has always thought his parents were James and Lily. Discovering Snape is his father would be a huge shock, and he might isolate himself to process this new information.
Another possible reason is that Harry could be feeling a sense of betrayal. He may think that if Snape was his father, why didn't he tell him sooner? This feeling of betrayal could lead him to isolate himself as he tries to sort out his emotions and figure out how to move forward.
Perhaps he's dealing with some sort of trauma. For example, after the many battles he's been through, like the fight against Voldemort, he may be suffering from post - traumatic stress disorder. To cope with this, he isolates himself from others as he doesn't want to burden them or he's just too caught up in his own dark thoughts.
One possible reason could be a misunderstanding. Maybe Naruto overheard something his family said that he misinterpreted as them not loving or believing in him. For example, if he heard them talking about his wild nature or his past mistakes in a way that he took the wrong way.
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.
It could be due to the trauma he has experienced. Losing friends and facing Voldemort multiple times has surely left deep scars. Isolating himself might be his way of dealing with the post - trauma stress. He needs time alone to heal and come to terms with everything that has happened.
One possible reason could be to hide his true identity. In the world of fanfiction, there might be threats or situations where he doesn't want to be easily recognized as Harry Potter. Maybe he wants to start anew, away from the fame and the constant danger associated with his name.
There might be some extremely dark and non - canon fanfictions out there with such a disturbing plot. However, this goes against the general spirit of the Harry Potter series. In the official story, Harry is a hero who overcomes great challenges. In a fanfiction with this idea, perhaps it could be due to extreme despair from losing too many loved ones or feeling an overwhelming burden of his destiny that he snaps and takes his own life. But again, this is a very unorthodox and sad take on the character.
One possible reason could be copyright infringement. If the fanfiction uses too much of the original 'Harry Potter' material without proper authorization, J.K. Rowling (or those in charge of the franchise) might take legal action. Another reason could be if the fanfiction misrepresents the characters in a way that goes against the intended spirit of the original work.
Well, it could be that he has lost all hope. In the fanfiction world, if the situation becomes so dire that he sees no way out for himself or the people he loves. For example, if Voldemort manages to gain complete control and Harry Potter thinks his sacrifice by taking his own life might be the ultimate solution to break Voldemort's power. He might also be suffering from post - traumatic stress after all the battles and losses, leading him to this extreme decision.
In the fanfiction, Harry Potter might live by himself because he is tired of the spotlight. After being in the public eye for so long, he desires a private life. He may also feel that living alone allows him to better understand himself and his powers. It could be that he has a prophecy or a personal quest that requires solitude. For example, he might be trying to master a very difficult and dangerous spell that he doesn't want anyone else to be in danger from if something goes wrong. Also, he could be exploring some dark corners of magic that the wizarding world might not approve of, and living alone gives him the freedom to do so without judgment.
Well, if Snape were Harry's dad in this fanfiction, Harry's isolation might take on a different tone. He could be more conflicted. Knowing Snape is his father, a man he had such a tumultuous relationship with before, would make him question his own identity. He might be more withdrawn as he tries to come to terms with this new family truth, and his relationships with his friends might become strained as he feels they couldn't possibly understand what he's going through.