One possible plot could be Naruto using his new Sage of Six Paths powers to take on the Akatsuki one by one. He could start with Hidan and Kakuzu, quickly dispatching them with his enhanced speed and strength. Then, he moves on to Deidara, outmaneuvering his explosive attacks with his own agility. Another plot might involve Naruto infiltrating the Akatsuki's hideout alone, using his shadow clones as decoys. He could then surprise Pain and defeat him in an epic battle, showing his growth as a ninja.
A great plot for this fanfiction could be that Naruto discovers a new jutsu specifically designed to counter the Akatsuki's powers. He first tests it on Sasori, easily breaking through his puppet defenses. As he progresses, he uses his unwavering determination and the power of friendship (yes, it's a bit cheesy but it works in Naruto) to defeat the rest of the Akatsuki. He could also have some sort of moral victory over Itachi, showing that his way of protecting the village is different but equally valid.
Pain would be one of the most challenging. His Rinnegan gives him a wide range of powerful abilities like the Six Paths of Pain. Naruto would have to figure out how to counter each of those paths and find a way to reach the real Pain. Itachi is also tough. His Sharingan and genjutsu skills are top - notch. Naruto would need to break free from his genjutsu and then find a way to fight back against his fire - based attacks.
One possible plot could be that Naruto is somehow mind - controlled by a powerful enemy who forces him to turn on Konoha. Maybe the enemy has a special jutsu that can manipulate Naruto's emotions and memories, making him believe that Konoha has wronged him in some way.
One interesting plot could be a story where Naruto tries to understand the Akatsuki's motives better and ends up befriending some of its members. This challenges his previous beliefs about them being all - evil.
Another plot might involve Naruto learning the secrets of the Akatsuki members. For example, he discovers how each member got their powers and tries to use that knowledge to his advantage. He could also form unexpected alliances within the Akatsuki, like with Sasori or Hidan, which would lead to some really cool and unpredictable story developments.
One exciting part could be the moment when Naruto first reveals his new strategy against Madara. It's like a turning point in the story where the tables start to turn. Another exciting bit might be the intense battle sequences where Naruto and Madara exchange powerful jutsu. The visual descriptions of their attacks colliding and the resulting explosions would be really thrilling.
One possible plot could be that the Akatsuki members, despite their villainous nature in the original Naruto story, see potential in Naruto. They start to train him in unique ways that the Leaf Village never thought of. For example, they might teach him some forbidden jutsu but also instill in him a different view of the ninja world, which causes Naruto to question the values he was brought up with in Konoha.
One interesting plot could be the sister having unique powers that she has to hide from the Akatsuki at first. Maybe she has a special ability to heal, which is both a blessing and a curse as the Akatsuki might want to use it for their own ends.
A common plot is Naruto using his friendship bonds to gain an edge. For example, in many fanfics, his bond with Sasuke becomes a key factor. Sasuke may return to Konoha and fight alongside Naruto against the Akatsuki. Another popular plot is Naruto unlocking some new, super - powerful form. Maybe a combination of all his different power - ups throughout the series that makes him nearly invincible against the Akatsuki.
Naruto would become more confident. After destroying Akatsuki, he'd realize his true potential. He'd know he can take on the toughest enemies and protect his village. This new - found confidence would also make him more respected among the other ninjas.
One common plot is the reader being a new recruit to the Akatsuki and having to prove themselves. They might face challenges from the other members, like Sasori being skeptical of their skills. Another plot could be a love story where the reader has a special connection with Itachi. He might protect the reader from the internal power struggles within the Akatsuki.