One possible plotline could be that Naruto discovers his connection to the Sannin later in his life. This new knowledge gives him access to hidden jutsu or knowledge that the Sannin had. For example, he might learn some unique medical ninjutsu from Tsunade. Another plot could involve Naruto facing enemies who are after the secrets that the Sannin might have passed down to him.
One possible plotline could be Naruto growing up with a different set of skills influenced by Tsunade. Since Tsunade is known for her medical ninjutsu and super strength, Naruto might have an earlier inclination towards medical skills. He could be trained in a more balanced way between combat and healing. For example, in battles, he not only uses his regular jutsu but also heals his comrades instantly on the spot. Another aspect could be the political influence. Tsunade being an important figure in the village, Naruto might have a different standing in the village hierarchy from the start and face different kinds of challenges related to leadership and decision - making.
One possible plotline could be Naruto discovering his connection to Kaguya later in his life. Maybe he starts having strange dreams or new powers start to emerge that he can't explain. This discovery could send him on a journey to learn more about his heritage and the Otsutsuki clan. It could also lead to a new level of understanding between him and Sasuke, as they both have ties to the ancient powers related to Kaguya.
One possible plotline could be that Madara's great - grandson discovers a hidden power within himself. Maybe he finds an ancient scroll left by Madara that contains a unique jutsu. He then has to train hard to master this jutsu while also facing off against new enemies who want the power for themselves.
In a 'naruto is logan's grandson fanfiction', a possible plotline could be that Naruto is initially unaware of his relation to Logan. As he grows and faces challenges, he starts to show signs of mutant abilities. This leads to a search for his true identity. Along the way, he could encounter other mutants or ninja who either help or hinder his journey. Another aspect could be that his unique powers attract the attention of powerful enemies from both universes, forcing him to team up with unlikely allies to defend himself and those he cares about.
One possible plotline could be that Naruto is lured into a trap by the Akatsuki. They use his overconfidence against him. Maybe they pretend to have a hostage that Naruto wants to save, and when he arrives, they overpower him with their combined jutsu. Another could be that they manage to find a way to nullify his Nine - Tails chakra, leaving him vulnerable to their attacks.
One possible plotline could be that Naruto's wings make him an outcast in the village at first. People are scared or jealous of his unique feature. But as he grows, he learns to use his wings in combat, perhaps in a new style of ninja fighting that combines aerial maneuvers. He could also use his wings to reach places quickly during missions, giving him an edge.
Well, a plot could involve Naruto facing challenges related to his new identity as a Senju. There could be those who oppose him having the Senju blood, perhaps out of jealousy or fear of his growing power. He might have to prove himself worthy of the Senju name. Also, his friendship with Sasuke could take on a new dimension. Since Sasuke is an Uchiha, there could be an interesting dynamic between the two clans' legacies within their friendship. Naruto could use his Senju powers to try and bridge the gap between the Uchiha and the rest of the village, as the Senju were often associated with peace - building in the past.
One possible plotline could be that Hinata is under some sort of mind - control. Maybe an enemy uses a jutsu on her that makes her see Naruto as a threat to the village in a false way. So, she kidnaps Naruto to stop him from doing something she believes is harmful. But as the story progresses, Naruto tries to break through to her real self and free her from the mind - control.
One possible plotline could be that Serafall, perhaps influenced by some external force or a misunderstanding, turns on Naruto. Maybe she believes Naruto has some hidden agenda that endangers her or her world. So she starts to undermine Naruto's efforts and even plots against him directly.
One possible plotline could be that Naruto is kidnapped by Kyuubi to gain some sort of power or knowledge from him. Maybe the Kyuubi believes Naruto has a secret that can help it break free from its current state. Another could be that Naruto is kidnapped as a way to get back at the Hidden Leaf Village, and the Kyuubi uses Naruto as a bargaining chip. It could also be that there is some external force that makes the Kyuubi kidnap Naruto, like a dark wizard or something similar that has control over the Kyuubi.