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.
In a fanfiction where Naruto kills the Akatsuki, it could lead to a much more peaceful ninja world much sooner. The Akatsuki's plan to capture the tailed beasts was a huge source of unrest. With them out of the picture, the villages might not be as paranoid about security. However, it could also lead to new problems. The power vacuum left by the Akatsuki could be filled by other evil forces or there could be internal power struggles within the villages that were previously united against the Akatsuki threat.
Well, perhaps in the fanfiction, Naruto kills Orochimaru and the Akatsuki, but it turns out that Orochimaru had a failsafe. His death triggers a powerful curse that starts to affect Naruto and the Hidden Leaf Village. Naruto then has to find a way to break this curse while also dealing with the remaining threats that were associated with the Akatsuki. It could be a race against time to save the village and himself.
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.
One possible plot could be that Naruto is somehow corrupted. Maybe he's been influenced by a powerful dark force or a powerful enemy has tricked him into believing that everyone is a threat to the world he wants to protect. So, he decides to take extreme measures and kill everyone to 'create peace' in his warped sense.
It could be that there is some sort of misinformation spread by an evil organization. They create false evidence that Batman is planning to destroy Naruto's village. Naruto, being the protector of his village, decides to take pre - emptive action. He tracks Batman down and in a fierce battle, kills him. But then as he starts to investigate further, he discovers the truth and has to live with the guilt of killing an innocent (in this case, Batman who was misrepresented).
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.
In this 'madara kills naruto fanfiction', the scenario might be set up in a way that the world around them has changed. Maybe there are new rules in the ninja world that Madara has adapted to better than Naruto. He could be using the political or social situation to his advantage. Additionally, the writer may have given Madara a different motivation that makes him more ruthless and determined to kill Naruto, and through a series of carefully crafted events, he manages to achieve this goal.
Well, in a fanfiction, the writer can bend the rules of the original Naruto universe. Maybe Kabuto could kill Naruto if he somehow got hold of a super - powerful and unexpected weapon or jutsu that nullified Naruto's abilities.
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.
Well, in a really dark and twisted fanfiction, Sasuke could be under some sort of mind - control spell. The spell could be so strong that it overrides his feelings for Naruto. He might then attack and kill Naruto without fully realizing what he's doing. But in the real Naruto lore, their friendship and mutual respect are so strong that this is highly unlikely.