The plot could involve Naruto using Samehada to gain an understanding of the Akatsuki's motives. Since Samehada has a connection to the Akatsuki through Kisame, it might hold some secrets. Naruto could use it to track down other Akatsuki members or find out more about their plans.
Perhaps Naruto has a different fighting style that Samehada finds more appealing. Naruto is known for his unpredictable and energetic combat, and Samehada might be drawn to that. It could also be that Naruto has a certain charisma or willpower that Samehada responds to on a more instinctual level.
In the fanfiction, it could be that Kisame gives Naruto Samehada as part of a deal. Maybe Naruto has to do something for Kisame in return. Naruto might struggle with the idea of making a deal with an Akatsuki member but decides it's worth it for the power of Samehada. Once he has it, he might face opposition from his friends and village elders who are suspicious of his new weapon and the way he obtained it.
Kisame would probably be very angry at first. Samehada is his weapon and has been with him for a long time. He might feel betrayed and try to get Samehada back by force.
Well, it could be about Samehada being overlooked in the Naruto universe. Maybe it's not being used to its full potential. For example, it might be that no one realizes its unique abilities aside from just being a weapon. Or perhaps it's being misused or underutilized by its owners.
The plot might be that an enemy steals Samehada and Naruto has to get it back. Along the way, he discovers that Samehada has a connection to an ancient and powerful clan. Naruto teams up with some members of this clan who want to reclaim Samehada as well. They face many challenges together, and Naruto uses his own skills and the power of Samehada to defeat the enemy. In the end, Naruto decides what to do with Samehada, whether to keep it or return it to the clan, depending on the bond he has formed with it.
One possible plot could be that Naruto somehow gets bonded with Samehada. Maybe during a battle in an alternate dimension where the laws of chakra and weapons are all jumbled. Naruto starts to learn how to use Samehada's unique abilities, like absorbing chakra not just to power himself but also to heal. This causes a stir among the ninja world as they see Naruto with this new and somewhat menacing power - the power to drain their chakra with ease. His friends are initially cautious but then come to realize that Naruto is still the same person inside and they work together to master this new form of power.
The plot could involve Naruto being shunned by the Hidden Leaf Village for some reason and Kisame, seeing an opportunity, takes him in. Kisame might see Naruto as a tool at first, but as time passes, he develops a sort of father - son bond with him. Naruto would then have to deal with the fact that he's now associated with the Akatsuki, which would put him at odds with his former friends. He could use this new position to try and change the Akatsuki from within, with Kisame's begrudging support.
In this fanfiction, perhaps Naruto is on a quest to learn more about Kisame. He could meet people who knew Kisame and through them, uncover secrets about his supposed father. This could lead to him having to make difficult decisions, such as whether to follow in Kisame's footsteps in some aspects or completely break away and forge his own path as a ninja.
Well, it could be that Naruto's relationship with the other Konoha ninjas changes drastically. They might see him as an outcast because of his association with Kisame. On the other hand, Naruto might try to bridge the gap between Konoha and the Akatsuki due to his upbringing by Kisame. This would create a whole new set of conflicts and alliances within the Naruto universe.
Well, in this fanfiction, Madara could give Naruto the Sharingan as a way to balance the power in the ninja world. Naruto then uses the Sharingan's ability to predict movements in combat. This gives him an edge against enemies who are used to his regular fighting style. He might also discover some hidden abilities of the Sharingan that no one else knew. For example, it could have a unique connection to his Nine - Tails chakra, creating a whole new set of jutsus.