A really cool plot twist could be that the main character's quirk, which was thought to be one thing, actually has a hidden secondary ability that is only unlocked under extreme emotional distress. This discovery not only changes the main character's fighting style but also their place in the hero hierarchy as they now have a much more powerful and unique ability.
One interesting plot twist could be a character who was thought to be a minor villain turns out to be a double agent working for the heroes all along. This completely changes the perception of their actions throughout the story.
One interesting plot twist could be the main character's gamer abilities suddenly evolving in an unexpected way. Maybe they gain a new power that completely changes the way they interact with the world of My Hero Academia. For example, instead of just having enhanced physical stats like in the game, they can now manipulate time briefly, which throws off all their enemies and allies alike.
Perhaps the mask has some sort of hidden power that the main character discovers by accident. For example, it might be able to manipulate time on a small scale, which could be used to turn the tides in a battle or save a life at a crucial moment.
One interesting plot twist could be that a former villain has reformed during the time skip and is now working secretly to protect the heroes from a new, unseen threat. This would turn the traditional hero - villain dynamic on its head.
Perhaps a plot twist where the power - up a hero gets is not what it seems. Instead of making them stronger in the way expected, it comes with some unforeseen side effects that make their journey more challenging. For example, if they gain a new quirk but it's slowly draining their life force while they try to figure out how to control it. This would create a lot of internal conflict for the character and also force their friends to find a way to help them without sacrificing the hero's life.
One interesting plot twist could be that the son of All Might actually has a quirk that seems weak at first but turns out to be extremely powerful in a unique situation. For example, his quirk might be the ability to sense danger, which initially makes him seem like a liability. But later, when facing an enemy who can hide their presence, his quirk becomes crucial for the heroes' victory.
A plot twist could be that the Quirk system and Stands are somehow related. Maybe there was an ancient event that split the power into two forms. This would open up a whole new exploration of the lore in both universes. Characters would have to reevaluate their understanding of their own powers and how they interact with those from the other universe.
A really interesting plot twist could be that the symbiote from the Spider - Man universe attaches itself to a major villain in My Hero Academia. This would make the villain even more powerful and unpredictable. The heroes would have to figure out how to deal with this new threat that has a combination of a quirk and the symbiote's abilities.
One of the most memorable characters could be the fan - made villain with a really unique quirk. Maybe they have the ability to manipulate time in a small area, which makes them extremely difficult to defeat. Their backstory of how they got their quirk and why they turned to villainy is also very engaging.
One interesting plot twist could be when a character from My Hero Academia ends up being a key figure in the Fate Stay Night world's power struggle. Maybe a hero's quirk is actually related to the magic system in Fate Stay Night in a way that no one expected.
One plot idea could be a villain who is secretly a double agent, working for the heroes all along. They infiltrate the villain group and gather information. Another idea is a hero who loses their quirk and has to rely on their wits and combat skills alone, like Batman in the DC universe. And a villain - hero team - up to face a greater threat that neither can handle alone.