In many fanfictions, Naruto might use new jutsus or a deeper understanding of his own power. Maybe he taps into a more powerful form of the Nine - Tails' chakra and combines it with his Sage Mode in a unique way to overpower Pain.
The village might experience a huge boost in morale. Naruto killing Pain would be seen as a major victory, and the villagers would feel safer. They would look at Naruto as an even greater hero, which could lead to more trust and unity within the village.
It could be a variety of villains. Maybe some of the traditional Naruto villains like Orochimaru or Pain could be in the story and Naruto kills them. Or perhaps in this fanfiction crossover, there are new villains created that are a combination of Naruto - style threats and Justice League - type menaces. It's hard to say exactly without reading the fanfiction, but it would be interesting if it included some well - known Naruto baddies being taken out by Naruto in a new setting with the Justice League around.
One consequence could be a shift in the power balance among the ninja villages. Since Orochimaru was a powerful and feared figure, his death might cause some chaos as his former allies or subordinates try to either avenge him or claim his resources. For example, some of his secret labs and experiments might be up for grabs, leading to potential conflicts.
In some fanfictions, Naruto's pain might manifest through his actions. For example, he could become withdrawn and isolate himself from his friends. This is because Naruto has always been a social person, so any deviation from his normal behavior could be a sign of his internal pain.
One possible cause could be his sense of failure. Naruto always wants to protect his friends and village, so if he fails in a mission or is unable to save someone, it can cause him great pain.
His fighting style could become more aggressive. Without the fear of pain, he might be willing to use more extreme techniques that would otherwise be too dangerous because of the pain they cause to the user. He could push his body to the limit more often.
Konan could be really interesting. In some fanfictions, she might have a different backstory or motivation that affects the Naruto vs Pain fight. For example, she could be secretly trying to stop Pain from going too far in his destruction of the Leaf Village.
Jiraiya could be a great addition. Since he was Pain's teacher, his presence could add a lot of depth to the story. He could offer insights into Pain's past and also help Naruto understand Pain better.
In a fanfic where Naruto kills Sirzechs, it could be a very interesting concept. Maybe it's a crossover universe where the power dynamics are completely different. Naruto, with his powerful jutsu, might have a reason like protecting his own world from a perceived threat by Sirzechs. However, it also depends on how the author has set up the story, the rules of the world they've created, and the motives given to Naruto for such a drastic act.