One possible storyline could be that Naruto's wife was killed during a major battle against a new and powerful enemy. This would send Naruto into a deep state of grief and depression, perhaps causing him to question his purpose as a shinobi. He might then embark on a journey to find the true cause of her death and seek revenge.
Maybe in the fanfiction, Naruto's wife was lost in a mysterious incident. She could have been kidnapped by a secret organization that was after Naruto's power. Naruto would then have to use all his skills and enlist the help of his friends to find her. He would be desperate and face many challenges along the way.
Perhaps his wife betrays him out of jealousy. She could be jealous of Naruto's status and the attention he gets. So she leaks some of his secret plans to the enemy. As a result, Naruto's missions start to fail and he becomes a target. He then has to face not only the external threats but also the heartbreak of his wife's betrayal. He might start to question his own judgment in choosing her as his partner.
It could be due to a power imbalance. If Naruto's power as Hokage makes her feel overshadowed or unimportant, she might be led to betray him. Also, perhaps she discovers some long - hidden secret about Naruto that she can't forgive, like a connection to a past enemy or some dark side of his shinobi past that he has kept from her.
Perhaps an old enemy from Naruto's past that was thought to be defeated has resurfaced. This enemy might have targeted Naruto's wife as a way to get revenge on Naruto for their previous defeats. They could be using her as a bait to lure Naruto into a trap.
One possible storyline could be that with his parents alive, Dark Naruto might not have turned so dark in the first place. His parents' love and guidance could have steered him away from the path of darkness. For example, Minato, being a powerful ninja, could have trained Naruto properly from a young age, and Kushina could have provided the emotional support he needed. This would change the whole dynamic of the Naruto universe as we know it, and there would be no need for him to seek power in dark ways.
Another idea could be that Naruto discovers some dark family secrets that he can't bear. This could include things like his family being involved in unethical experiments in the past. The shock and disappointment are so great that he loses control and ends up causing harm to his family, though it's a very tragic and complex situation.
Perhaps in the fanfic, Naruto loses his arm due to a curse or a forbidden jutsu gone wrong. His friends, like Sasuke, then try to find a way to either get him a new arm or help him come to terms with the loss. It could also show Naruto's journey to adapt to his new disability and still be a great ninja, inspiring the younger generation in the process.
One possible storyline could be in a dark AU (Alternate Universe). Maybe there's a powerful new enemy that targets Hinata specifically because of her connection to Naruto. This enemy could have some sort of vendetta against the Hyuga clan and sees Hinata as the key to their downfall. Naruto is then left to deal with the grief and also find a way to avenge her death, which could lead to a whole new arc of him exploring darker powers or making some difficult moral choices.
Another storyline could be that Naruto is wrongly accused of a crime he didn't commit in Konoha. Disillusioned with the village that once supported him, he becomes a ronin. He then meets other outcasts along his journey who have similar stories. Together, they form a sort of vigilante group that helps those who are oppressed by unjust ninja villages.
One possible storyline could be Naruto somehow getting his hands on a Murcielago (assuming it's a vehicle or some sort of powerful object in this fanfic). He might use it to gain an edge in his ninja battles, perhaps modifying it with his ninja skills. For example, he could add some chakra - powered enhancements to its speed or defense capabilities.
One possible storyline could be that Naruto somehow ends up in Mizore's world. Maybe through a strange jutsu gone wrong. He could then use his ninja skills to help Mizore in her own adventures, like fighting off some new threat that her world is facing.