Maybe it's a hero and a villain who get cuffed together accidentally. This could lead to some interesting character development as they start to understand each other's motives. For instance, if Todoroki was cuffed to a minor villain. Todoroki might learn more about the reasons some people turn to villainy while the villain could see that heroes aren't all bad.
Another plot could involve a group of heroes in training getting cuffed together during a practice exercise gone wrong. They have to figure out how to use their combined quirks to get free. Like if Uraraka, Iida, and Tsuyu were cuffed. Uraraka could use her zero - gravity quirk to make movement easier, Iida could provide the speed, and Tsuyu could use her long tongue for various tasks.
All Might and Shigaraki. It would be really interesting to see the symbol of peace cuffed to the main villain's apprentice. All Might could try to influence Shigaraki and show him a different path, while Shigaraki would be in a position where he has to face the hero he's been taught to hate up close.
One idea could be that two rival Pokemon trainers are cuffed together by a mischievous Pokemon. They have to learn to work together to escape and in the process, they discover new things about each other's training styles. For example, one trainer might be more focused on attack power while the other on defense. Through this forced cooperation, they might even combine their strategies to create a new and powerful way of battling.
One plot idea could be that the heroes and villains get stuck in an alternate dimension together. They have to put aside their differences to find a way out. Maybe they discover a common enemy within this new place.
Another possible theme is self - discovery. The characters may learn new things about themselves or each other while being in this unique 'cuffed together' situation. It could force them to confront their fears, weaknesses, or hidden strengths, and this journey of self - discovery can be a central part of the fanfiction.
I'm not sure about specific 'little witch academia cuffed together fanfiction'. But you can try searching on fanfiction websites like Archive of Our Own. There are likely to be some interesting works there.
How about a fanfiction where the villains and heroes have to team up? There could be a greater threat, like an alien invasion or a powerful quirk - user who is out to destroy the entire world. The heroes and villains realize that they can't defeat this threat alone, so they put aside their differences. This would lead to some really interesting character interactions, like Bakugo having to work with Shigaraki and both of them learning to respect each other's skills despite their opposing natures.
One possible plot could be that the Powerpuff Girls Z are cuffed together by some villain's new device. They have to work together in a more restricted way to fight crime. Maybe they struggle at first with the lack of individual movement but then learn to combine their powers even more effectively in this new situation.
An interesting plot could involve an anti - hero who has a hidden agenda that is not entirely evil but also not in line with the traditional hero goals. Maybe they are trying to expose a corrupt part of the hero society from within. They could form alliances with some villains who also have a vendetta against the corrupt elements. This would create a complex web of relationships and moral dilemmas.
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.
Maybe a plot where a group of Warhammer heroes are sent to the Hero Academia world to stop a chaos invasion that is starting to seep into that realm. They have to work with the local heroes, sharing their knowledge of dark magic and ancient weapons to combat the new threat. This would involve a lot of cultural clashes and learning experiences between the two groups.