Maybe Naruto discovers some dark secrets about his family that completely shatter his world view. For example, he finds out that his father was involved in some really bad things. This revelation makes him question everything he believed in and he becomes emo as a result. He might start wearing darker clothes, cutting off his hair, and his behavior towards others becomes cold and distant.
In a 'Naruto is emo' fanfic, the plot could revolve around Naruto being constantly rejected by the villagers despite all his efforts to protect them. He starts to feel like an outcast again, just like when he was a child. This constant feeling of being unloved and unwanted makes him turn emo. He might start writing dark poetry, expressing his inner pain, and his ninja skills might even be affected as his focus shifts from being a hero to dealing with his own emotional turmoil.
Maybe Naruto discovers some dark secrets about his family that completely shatter his positive outlook. For example, if he finds out that his father was involved in some unethical experiments. This revelation could send him into an emo state where he questions his identity and purpose.
One possible plot could be that Mikoto somehow survived and she takes Naruto under her wing. She trains him secretly, using her Uchiha knowledge to make him stronger. This could lead to Naruto having a unique set of skills that no one else has.
Well, one possibility is that Naruto resigns due to feeling burnt out from all the battles and political unrest in the village. He might decide he's done his part and wants a simple life away from the chaos.
One possible plot could be that Naruto is wrongly accused of a crime he didn't commit. Maybe he was framed by an old enemy who wants to see him suffer. While in prison, he tries to prove his innocence. He could use his ninja skills subtly to gather evidence within the prison walls, and also make some unlikely allies among the inmates who start to believe in his innocence as they get to know him better.
In a 'naruto is a uchiha fanfic', a possible plot could be that Naruto is so inspired by the Uchiha that he tries to bring back the glory of the clan. He starts by trying to understand their culture and values better. He could try to convince the village to support the revival of the Uchiha name. This would likely involve him dealing with the political aspects of the village as well as any lingering grudges against the Uchiha. He may also have to face off against those who would rather see the Uchiha stay in the past, all while learning more about the Uchiha's unique abilities and trying to incorporate them into his own fighting style.
There are probably 'naruto is evil' fanfics out there. A possible plot could be that Naruto is influenced by some dark force. This force twists his perception of right and wrong. As a result, he starts to target his former friends and allies. He might use his skills to cause chaos in the ninja world, believing that the current system is corrupt and needs to be overthrown.
Perhaps Naruto gets corrupted by some dark force. It changes his personality completely. He might start seeing all the people in the Hidden Leaf Village as the source of his problems. He could remember all the times he was ostracized as a child and now blames everyone for it. So in the fanfic, his hatred for everyone grows as he views the world in a new, darker light.
A plot might be that Naruto is born in the Naruto universe but has dreams and visions of Sparda. As he grows, he starts to show extraordinary powers that are not normal for a ninja. He then embarks on a journey to find out who Sparda is and discovers that he is his father. Along the way, he meets characters from the Devil May Cry universe who help him understand his powers. He has to fight against ninja clans who want to use his powers for their own gain and demons who want to corrupt him. He uses his Naruto - like tenacity and Sparda - inspired powers to overcome all these obstacles.
Well, perhaps Naruto could use his ninja skills in the way Zhuge Liang used his military strategies. For example, Naruto might outwit his enemies in battles like Zhuge Liang did with his brilliant tactics in ancient Chinese warfare. He could set up traps and use deception, just as Zhuge Liang was famous for his empty city ruse.
One possible plot could be that in a crossover world, Naruto is somehow neglected by his usual friends and allies. Meanwhile, a Yugioh character, perhaps Yugi, stumbles into this world. Yugi notices Naruto's situation and decides to use the power of the Millennium Puzzle to help Naruto regain his confidence and the respect of those around him. They form an unlikely friendship and together face challenges that the neglect has caused, like Naruto having to prove himself all over again in battles.