Perhaps Naruto has a secret life as an artist. He might be using his skills to draw portraits of his friends and the beautiful landscapes of the Hidden Leaf Village. He keeps it a secret because he's shy about showing his creative side in a ninja - dominated world.
One possibility is that Naruto has a secret relationship with a character from another village. This relationship has to be kept under wraps due to the political tensions between their respective villages. They meet in secret places to spend time together, away from the prying eyes of their comrades and leaders.
It could be that Naruto is secretly training a new and powerful jutsu that he doesn't want anyone to know about yet. Maybe he's afraid that if his enemies find out, they'll try to stop him before he perfects it.
One possible plot could be that Naruto discovers he has a child during a mission. Maybe he saved a village years ago and unknowingly had a relationship with a local woman. The child could be in danger from some villains who want to use the child's connection to Naruto for their own evil plans.
Well, perhaps the story could be about Naruto finding out he has a sister who was hidden away for her own safety. Maybe she has some unique powers that the villains are after, and Naruto has to protect her while also learning about his family's past.
It could be that a new character, someone from a far - off land that Naruto met during one of his travels, is involved in his secret life. This character could bring with them a different culture and set of skills that Naruto is learning from in secret, perhaps something that could revolutionize the way ninjas in the Hidden Leaf operate.
It could be Hinata. In the original series, Hinata has a deep affection for Naruto. In a fanfiction, it would be a natural progression for her to be his secret fiance. Maybe they got engaged secretly to avoid some political unrest in the village.
It might also be Gaara. Their initial encounters were filled with tension, but as the story could be twisted in fanfiction, that could develop into a different kind of relationship. Gaara's own journey of self - discovery and Naruto's influence on him could be a basis for a romantic relationship in fanfic.
Well, in a 'Naruto has secret mission' fanfiction, Naruto could be tasked with establishing an alliance with a reclusive and powerful clan. This would require him to prove himself worthy and overcome their initial distrust. He may also be on a mission to find a long - lost jutsu that could change the balance of power in the ninja world, and he has to keep it a secret from other villages to prevent a scramble for it.
One possible plot could be that Fem Naruto has been in hiding with her child to protect it from old enemies. Maybe she was in a relationship during a time of peace but things turned bad. Now she's constantly on the move, training her child in secret ninja skills.
One possible storyline could be that Naruto discovers he has a daughter in a very unexpected way. Maybe she was hidden away by an enemy for some dark purpose. As Naruto uncovers the truth, he has to deal with his own guilt for not knowing about her and also protect her from those who would still do her harm.
One plot line might be that Naruto has a secret mission to protect a sacred object that has been hidden from the ninja world. This object could hold the key to some great power or knowledge. He has to keep it a secret from everyone, including his friends, and this creates a lot of internal conflict as he struggles to balance his loyalty to his friends and his duty to protect the object.
It could be a random villager that Naruto met during one of his travels. Maybe she was from a small village that Naruto helped protect, and they had a brief encounter that led to the child.