Well, it could happen if Naruto has some sort of special weapon. For example, he might get a sword that can disrupt Hidan's connection with his voodoo - like powers. Once that connection is broken, Naruto could easily defeat and kill Hidan. Also, Naruto's growth in chakra control and strength could play a role. With his enhanced abilities, he could overpower Hidan and deliver a fatal blow.
One possibility is that Naruto has studied Hidan's abilities thoroughly. He discovers the weakness in Hidan's immortality, which is related to the ritual he performs. Naruto then creates a situation where Hidan is unable to complete the ritual. Without the ritual, Hidan is vulnerable. Naruto takes advantage of this moment and uses his Rasengan or some other powerful attack to kill Hidan. In fanfiction, the author has the freedom to explore different scenarios and character developments that can lead to such an outcome.
The Akatsuki would surely be affected. They would lose one of their members, which could disrupt their plans. Also, it might change the way other characters view Naruto. Some might see him as a more formidable threat, while others might see him as a hero for taking out a dangerous enemy.
Well, in a fanfiction scenario where Naruto is raised by Hidan, the first thing to consider is the influence on Naruto's values. Hidan has his own set of beliefs that are very different from what Naruto was taught in the village. Naruto could end up being more of an outcast in the shinobi world as his actions and attitude would be shaped by Hidan. His ninja training would likely be more focused on survival and combat in a very different way. He might not have the same bond with his friends as in the original story, as Hidan is not exactly a team - player. Also, Naruto's chakra nature might be developed in a unique way, maybe more attuned to dark or unorthodox forms of jutsu due to Hidan's influence.
If Naruto becomes a Hidan fan in fanfiction, it would be a total shift in his character perception. Naruto has always been about friendship and protecting others, while Hidan is a bloodthirsty and somewhat insane character. Maybe Naruto would see Hidan's fearlessness in battle as something to look up to. But he would also have to grapple with Hidan's immoral actions, like sacrificing people. This could lead to an internal conflict within Naruto as he tries to reconcile his new - found 'admiration' with his own moral code.
Well, in a fanfiction scenario, Naruto might kill Aizen if he manages to use his shadow clones to outwit Aizen's illusions. Naruto could also use his Sage Mode to sense Aizen's reiatsu and counter his attacks. Maybe he combines his Rasengan with some new jutsu he's developed specifically to deal with Aizen's powers.
In fanfiction, Naruto might kill a god through the power of his strong will and the unique abilities he has. For example, his Sage Mode could be enhanced to a level that allows him to overpower a god - like entity. Also, his Nine - Tails chakra could be combined with some new, made - up powers in the fanfiction world to give him the strength needed.
In a Naruto kills Thanos fanfiction, Naruto's sealing techniques could play a major role. He could use sealing jutsu to seal away Thanos' powers or even Thanos himself. Naruto has experience in dealing with powerful foes and sealing them away. Also, Naruto has the ability to sense danger and react quickly. Thanos, on the other hand, may underestimate Naruto at first. By the time he realizes Naruto's true strength, it could be too late for him.
Another possibility is a complete character distortion in the fanfiction. The writer might decide to create a 'bad Naruto' version where he has lost all his positive traits. However, this is quite far - fetched considering the strong foundation of Naruto's character in the original series. It would be a very different and probably controversial take on the Naruto - Hinata relationship.
Naruto himself might face a moral dilemma. Killing a God of Destruction, even in a fictional context, could weigh heavily on his conscience. He might have to deal with the guilt and the consequences of his actions, especially if there are other characters who oppose his decision or if there are unforeseen side - effects.
In some fanfictions, Naruto might kill Orochimaru by overpowering him with newfound powers. For example, if Naruto has a sudden boost in his Sage Mode or a new jutsu he developed. Orochimaru is a powerful foe, but Naruto's growth could potentially lead to his defeat. Maybe Naruto has also mastered some sealing techniques that can counter Orochimaru's ability to regenerate and transfer his soul.
In a fanfiction scenario where Naruto kills Hanzo the Salamander, it could be due to Naruto's newfound power. Maybe he has mastered a powerful jutsu that gives him the upper hand. For example, if he has a super - charged Rasengan that can break through Hanzo's defenses. Another possibility is that Naruto has allies who help him set up a perfect trap for Hanzo. He could be strategizing with Shikamaru, who comes up with an elaborate plan to outwit Hanzo.