One possible plot could be Naruto believing that by joining the Akatsuki, he can change them from the inside. He might think that his influence can stop their more evil plans. For example, he could try to convince them to stop collecting the tailed beasts in a violent way.
Kabuto could be an antagonist as well. He is a power - hungry character. If Naruto is trying to bring positive change to the Akatsuki, Kabuto's thirst for power and his underhanded tactics could put him in direct conflict with Naruto, as he might see Naruto as a threat to his own plans within the Akatsuki.
In a fanfiction where Naruto joins the Akatsuki, there could be a lot of interesting character interactions. He would be in close quarters with villains like Sasori or Hidan. Naruto might try to learn more about their pasts and what led them to become members of the Akatsuki. This could also cause a rift in his relationships with his old friends in Konoha. They might see him as a traitor, while Naruto is actually trying to bring about change in the Akatsuki for the greater good.
For such a plot to be possible in the fanfiction, it could involve some major changes in the Naruto world. The Akatsuki could have some new secret weapons or techniques. Also, Naruto might be in a situation where he is not able to access his full power, like being poisoned or something. And perhaps the Akatsuki are more united and desperate than ever to achieve their goals, leading them to take out Naruto who is a major obstacle for them.
It could be that Naruto has a vision of a different kind of life or place where he can truly be at peace. He might meet someone from another village or group who shows him an alternative way of living that is more appealing than staying in Konoha. And so, he gives up on Konoha to pursue this new path.
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.
In this fanfic, it could be that Naruto creates the mini - version of himself accidentally. Tenten finds the mini - Naruto and at first is a bit confused. But then she realizes he has all of Naruto's positive traits like his determination. So she decides to keep him around. They go on little adventures together in the village, and the mini - Naruto might even get into some comical mischief that Tenten has to get him out of.
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.