In a fanfiction, Naruto and Sasuke in Akatsuki might have a story where they are sent on a special mission together by the Akatsuki leaders. Along the way, they face many challenges that test their bond. Sasuke might initially be more in tune with the Akatsuki's ways, but Naruto tries to convince him to find a better path. As they complete the mission, they start to change the Akatsuki's ideology bit by bit.
Well, the fanfiction could start with Naruto and Sasuke being kidnapped by Akatsuki. Once in the organization, they are separated at first. Naruto, being his usual self, tries to befriend the other members and understand their motives. Sasuke, on the other hand, is more focused on finding a way out. But as time passes, they reunite and realize that they can use Akatsuki's resources and manpower to fight a common enemy that they discover is planning to destroy the ninja world. So they stay in Akatsuki, but with their own hidden agenda.
Well, one possible plot could be that they join initially to spy on Akatsuki from the inside. Naruto might think he can change the Akatsuki members' minds with his talk - no - jutsu. Sasuke could be there to find out more about the secrets Akatsuki is hiding, especially those related to his family. Maybe they end up causing chaos within Akatsuki as they slowly turn some of the members towards a more positive path.
One possible plot twist could be that Naruto and Sasuke join Akatsuki with the secret intention of reforming it from within. They might want to change the organization's goals from causing chaos to actually protecting the shinobi world in a different way. For example, they could try to use Akatsuki's resources and manpower to fight against a greater threat that the traditional shinobi villages are ignoring.
A plot twist could be that Akatsuki has a hidden agenda that Naruto, Sasuke and Sakura are unaware of when they join. Maybe Akatsuki is being controlled by an even more powerful and sinister force, and the three are lured in as pawns. They then have to figure out the real situation and fight not only against the Akatsuki members who oppose their reform ideas but also against this hidden power.
One possible plot could be Naruto joining the Akatsuki under some false pretense. Maybe he's trying to infiltrate them to gather intelligence for the Leaf Village. He'd have to keep his true identity and motives hidden while interacting with the dangerous members like Itachi and Kisame.
A plot twist might be that Naruto discovers that the Akatsuki was actually formed with good intentions in the past, but got corrupted over time. As the leader, he decides to go back to the original purpose. He then has to fight against the current power - hungry members while also trying to convince the other villages that the Akatsuki can be a force for good again. This would create a lot of tension and interesting character dynamics.
One possible plot twist could be that Naruto joins the Akatsuki to spy on them for Konoha. But as he spends more time with the members, he starts to understand their motives, which are not all as evil as he initially thought. For example, some might be seeking revenge for past wrongs done to their villages.
One possibility is that Naruto joins Akatsuki to change it from within. He might think he can stop their more evil plans while also learning more about his own powers and the secrets of the ninja world that Akatsuki seems to be involved in.
Well, if Naruto joins Akatsuki in fanfiction, perhaps it's because he's disillusioned with the Hidden Leaf Village for some reason. Maybe he feels betrayed by them. In Akatsuki, he could form unexpected alliances. For example, he might bond with Hidan over their shared brashness in a way, and together they could influence the direction of Akatsuki's actions.
Maybe Naruto joins the Akatsuki with the intention of spying on them for Konoha. He could pretend to be on their side while secretly sending information back to his village. This would add a lot of tension and secrecy to the story as he has to constantly be careful not to be discovered.
The plot could be Naruto getting cursed by a jutsu that makes him have to wear the Akatsuki cloak to survive. As he wears it, he slowly starts to understand the Akatsuki's ideology from a different perspective. He then tries to change the Akatsuki from within, using his own values to influence the members.