All For One could be a great main antagonist. He's already extremely powerful and his desire for chaos and control could easily lead to an apocalyptic situation. He might find a way to spread his influence even more, perhaps by taking over the minds of many at once.
Tomura Shigaraki is also a likely candidate. If he were to fully embrace his power and his hatred for society, he could cause an apocalypse. He might start by destroying major cities and then continue to spread destruction across the world. His decay quirk could be used in very destructive ways on a large scale.
All Might could also be a main character in a bnha alien fanfic. His status as a symbol of peace in the BNHA world could be extended to an intergalactic scale. He could be the one to bridge the gap between humans and aliens, using his experience and power to negotiate and fight when necessary. His weakened state could even be a plot point, as he has to rely on new alien technology or powers to regain his strength and continue to protect.
Midoriya could be a great main character. His growth throughout the series makes him a natural choice. His graduation could be about finally proving to himself and others that he has become a great hero, ready to face the world on his own.
Perhaps an all - powerful villain from another dimension invades. This villain has the ability to control the minds of those with quirks and uses them to fight against the remaining heroes. He wants to take over the 'My Hero Academia' world and remake it in his own image. His powers are so strong that it takes all of the heroes' combined efforts just to try and figure out a way to stop him.
Perhaps a group of radical wizards who believe that the apocalypse was a sign that the old ways of the wizarding world were wrong. They want to create a new order, even if it means using cruel and unethical magic. They see the more traditional wizards, like those who were friends with Harry Potter, as enemies who are holding back progress.
Perhaps a group of anti - technology extremists could be the main antagonists in an Ultron fanfic. They see Ultron as the symbol of all that is wrong with technology and are determined to take him down, no matter the cost. They might use their own advanced, but more rudimentary, technology to fight against Ultron. This would create an interesting contrast between Ultron's high - tech abilities and their more basic, yet effective, methods.
Uraraka could be a main character as well. Her zero - gravity quirk could be used in interesting ways, like floating ingredients to make it easier to assemble sandwiches or helping to clean up spills by making the dirty items float into the trash can without having to touch them.
Dabi would also work well. His vendetta against Endeavor could be a starting point for his reform. As he discovers more about his family and the truth behind his father's actions, he might decide to change his ways and use his power for good instead of revenge.
The offspring of Todoroki and Momo could be great main characters. With Todoroki's ice - fire quirk and Momo's creation quirk, their child might have a really unique and powerful combination of abilities. The character could struggle with the high expectations that come from having such powerful parents.
Deku could be a main character. Since his whole journey has been centered around his quirk, losing it would be a huge deal. He would have to face the fact that all his training and growth related to his quirk was now useless, and he'd have to start from scratch in a different way.
A rival medicine cat from another Clan might be the main antagonist. They could see Alderheart as a threat to their own status or the well - being of their Clan. So they might use dark magic or some underhanded tactics to bring about his death.