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 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 feeling extremely lost and having to find his own way to become stronger without their guidance. He might start to question his own worth and abilities, but then he could meet new allies who help him realize his true potential on his own. For example, he could encounter some other outcast ninja who have their own unique skills and together they form a new kind of ninja team that challenges the traditional ways of the ninja world.
Another plotline might be that Tsunade is affected by some kind of dark magic or genjutsu that makes her turn against Naruto. Naruto, realizing it's not really Tsunade's fault, still has to fight her to try and break the spell. He could call upon his friends for help, but in the end, it's his determination and his bond with Tsunade that helps him reach her and break the control.
One possible plotline could be that Naruto leaves with Tsunade on a mission to find a rare herb that is said to have the power to heal any wound. Along the way, they face various enemies who also want the herb for their own malicious purposes. Naruto's skills and Tsunade's wisdom would be put to the test as they battle their way through.
Perhaps a plot twist would be that there is some sort of curse associated with Naruto's lineage as their grandson. This curse could be related to the same forces that Tsunade and Jiraiya fought against in their lives. Naruto has to struggle not only with his normal ninja duties but also with this hidden curse. It could manifest in strange ways, like affecting his chakra control or making him a target for certain enemies. On the other hand, it could also be a source of great strength if he can overcome it. And there could be a prophecy related to him being the grandson of Tsunade and Jiraiya that he has to fulfill, which adds another layer of complexity to the story.
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.
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 Tsunade teaching Naruto more about medical ninjutsu. Since she is a great medical ninja, she could pass on her knowledge to Naruto, which would add a new dimension to his skills. Another aspect could be her guiding Naruto in leadership, as she is the Hokage. This might help Naruto in his future role as a leader in the village.
Perhaps in the fanfic, Futa is a new character in the Naruto world who has some sort of connection to Tsunade's past. Naruto gets caught in the middle of their relationship. It could involve Futa having some secrets that Tsunade is desperate to know, and Naruto helps in uncovering those secrets while also growing as a ninja himself.
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.