It could be the old enemies who see Naruto's new form or role as a threat. Maybe Orochimaru, who is always after power, would try to stop Naruto or take advantage of his new state. He might think Naruto's power in this apocalyptic scenario can be harnessed for his own evil purposes.
Well, perhaps Naruto becomes the new apocalypse in a sense that he has been corrupted by some powerful evil force. His friends would then be in a dilemma of having to either stop him or try to save him. His transformation could also lead to a new power hierarchy in the ninja world, with everyone fearing his new, unpredictable abilities.
The apocalypse in the fanfiction could be a result of a failed experiment in the ninja world. Naruto, being the hero he is, tries to find a way to reverse the situation. He embarks on a journey to discover the source of the apocalypse. Along the way, he meets new characters who are also survivors. He has to use his knowledge of ninjutsu in new and creative ways to overcome the challenges of this post - apocalyptic world.
Maybe Harry Potter has to use his magic to fight against the apocalyptic disasters like hordes of dark creatures or a spreading deadly magic. He could gather his friends and allies from Hogwarts and the wizarding world to try and stop the end of the world.
Naruto's normally positive and upbeat character might become more hardened. He'd be more cynical after seeing so much destruction. His trust in others might be shaken, especially if he's been betrayed during the apocalypse.
One possible aspect of 'Naruto Son of Apocalypse' fanfiction could be exploring how Naruto's character is re - imagined with apocalyptic powers. Maybe he has the ability to control dark forces or has a more brooding and serious personality. For example, his Rasengan could be infused with some sort of apocalyptic energy that makes it far more destructive than in the original series.
The characters would change in many ways. Harry Potter, who has already faced so much, would become more of a survivalist. He might be more willing to take risks that he wouldn't have before. Hermione would likely turn into a strategic mastermind, thinking several steps ahead to counter the chaos of the apocalypse. Ron, on the other hand, would probably develop a more serious side. No longer could he rely on just his loyalty and friendship; he'd have to be a fighter. Neville, who has shown great courage in the original series, would become a symbol of hope, inspiring others to keep fighting. And the villains, if any are still around, would either try to take advantage of the apocalypse or be forced to side with the heroes in order to survive.
He probably gains the ability to control the chakra of the Kyuubi more freely. This could mean enhanced strength, speed, and reflexes. He might also be able to use some of the Kyuubi's unique jutsu like the Tailed Beast Ball. His healing factor could be improved as well, allowing him to recover from injuries faster.
Kakashi could also be a great help. With his vast experience and wisdom, he could guide Naruto in understanding the implications of becoming a new species. He might be able to teach Naruto how to control any new powers that come with the transformation and how to deal with the potential social isolation.
One possible new character could be a young orphan with a hidden talent for ninjutsu. Naruto, having been an orphan himself, takes the kid under his wing. This new character could have a unique power that is related to illusions but in a much more advanced and dangerous way than the normal genjutsu. Another new addition could be a ninja from a rival village who, after seeing Naruto's growth, decides to join him instead of fighting against him. This character could bring with him the knowledge of the rival village's secret ninja strategies.