One possible plotline could be Naruto discovers some ancient scrolls that detail Indra's life and achievements. He becomes so inspired by Indra's strength and leadership that he starts to model his own ninja way after him. For example, Naruto might try to incorporate Indra's strategic thinking into his battles against new and powerful enemies in the ninja world.
In a fanfiction, Naruto could be an Indra fan in a more spiritual sense. He might have a vision or dream where he meets Indra. Indra imparts some wisdom to Naruto about the nature of power and how to use it for the greater good. This then changes Naruto's perspective on his own power as a jinchuriki and how he should interact with the other ninja villages.
One possible plotline could be Fem Indra being a time - traveler and changing the course of Naruto's story. For example, she could prevent some of the major tragedies that occurred in the original Naruto storyline.
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.
Well, perhaps the story could focus on Naruto's internal conflict. At 12, being a Jounin is a huge deal but being neglected means he has to deal with self - doubt. He could start to question his own abilities and his place in the village. As a result, he might seek training from unlikely sources outside the village, which would add an interesting twist to the story.
One possible plotline could be that Naruto is adopted by an Uchiha family early on. This changes his entire upbringing. He might be trained in the ways of the Uchiha from a young age, learning their unique fire - style jutsu and the secrets of the Sharingan much earlier. It could also lead to him having a different relationship with Sasuke, as they would be family in a sense. Maybe Naruto would be more in tune with the Uchiha's history and the tragedy that befell them, and this could fuel his determination to protect the village in a new way.
One possible plotline could be that Cloud, with its unique culture and way of life, would introduce Naruto to a whole new set of values. Naruto might struggle at first to adapt to the more reserved nature of the Cloud ninja. For example, he could have trouble fitting in with their strict training regimens that are different from what he's used to in Konoha. Another aspect could be his relationship with the other ninjas in Cloud. He might form an unexpected bond with a fellow outcast ninja, and together they could work towards changing some of the old - fashioned views in Cloud.