A possible plot could involve the main characters of both franchises swapping roles. For example, the Persona protagonists find themselves in the Danganronpa school, having to deal with the killing game while the Danganronpa characters end up in the Persona cities, trying to understand and use their newfound Persona powers. This would lead to a lot of character development and interesting interactions as they adapt to their new environments.
Maybe the Velvet Room attendants from Persona start showing up in the Danganronpa setting. They offer the students a chance to awaken their Personas, but there's a catch - they have to face a series of trials similar to the class trials in Danganronpa. This could create a really unique and tense situation.
One idea could be the characters from Persona 4 and Persona 5 swapping their worlds. So the Phantom Thieves end up in Inaba and have to deal with the Midnight Channel mystery. And the Investigation Team finds themselves in Tokyo and gets involved in the Metaverse. It would be really cool to see how they interact with the different environments and characters.
One idea could be to cross Danganronpa 2 with another popular game like Persona. The characters from Danganronpa 2 could find themselves in the world of Persona, dealing with the Shadows and having to adapt their skills. For example, Hajime could learn to use a Persona and use his detective skills to solve the mysteries related to the Dark Hour. Another plot idea could be a crossover with a fantasy world. The Danganronpa 2 characters are transported to a magical realm where they have to face new challenges. Maybe they have to fight dragons or solve magical riddles, all while still dealing with the underlying distrust and mystery that is characteristic of Danganronpa. A third idea is to cross it with a post - apocalyptic world. They have to survive in a desolate landscape, find resources, and deal with new threats, all while trying to figure out if there's a way to get back to their own world.
A really interesting plot could involve a new threat that emerges and can only be defeated by combining the powers and skills of the Persona 3 and 5 characters. For example, the combat styles of the two groups are different. The SEES members are more used to fighting in the Dark Hour, while the Phantom Thieves operate in the cognitive world. They would need to learn from each other's strategies. And on a character level, the more serious and reserved characters from Persona 3 could interact with the more flamboyant and confident characters from Persona 5, leading to some really interesting dialogue and relationship building.
Maybe there's a situation where the Velvet Room attendants from Persona 3, 4, and 5 realize that there's a threat to the collective unconscious that only the combined efforts of the three protagonists can stop. So, they somehow manage to bring the characters together. The characters then start to learn from each other's combat styles and ways of forming bonds with their friends, which helps them in their fight. For example, the protagonist of Persona 3 could teach the others about his experiences with death and how to face it head - on in battle, while the Persona 4 protagonist could share his knowledge of reading people and finding the truth behind the mysteries. The Persona 5 protagonist could contribute with his skills in stealth and infiltration.
A great plot for Persona 4 crossover fanfiction could be a crossover with the 'Sword Art Online' universe. The Persona 4 gang could be trapped in the virtual world of SAO and have to use their Personas to defeat the bosses and escape. Or, they could cross over with the 'My Hero Academia' world. Here, they could attend the hero school and learn new ways to use their powers, while also sharing their Persona knowledge with the MHA characters. Also, a crossover with 'Harry Potter' would be interesting. They could attend Hogwarts and discover that their Personas have unique interactions with magic.
A crossover with a post - apocalyptic world setting. The Persona 3 characters find themselves in a world destroyed by some great cataclysm. They have to use their Personas not only to fight the Shadows that lurk in this new world but also to survive against other desperate survivors and new, mutated threats. They might also have to find a way to restore the world using their Persona powers.
A cool plot could involve a powerful Persona user from Persona 3 who has somehow lost their memory and ends up in Inaba (the setting of Persona 4). The Investigation Team from Persona 4 takes them in and tries to help them regain their memory. As they do, they discover that this person holds the key to preventing a major catastrophe that will affect both their worlds.
You could do a crossover with the Final Fantasy series. Picture the Danganronpa characters in a world filled with magic, summons, and complex job classes. They might have to complete quests or battles to progress, and the killing game aspect could be intertwined with the battles against powerful Final Fantasy monsters. For example, the murderer could gain power-ups from defeating certain bosses.
One idea could be the Persona characters getting sucked into the JJBA universe. For example, the Phantom Thieves could end up in Morioh and have to deal with Stand users while trying to find a way back home. They might team up with Josuke and his friends to fight a common enemy that's causing chaos in both their worlds in a strange way.
Maybe the Persona users' powers start to malfunction in the RWBY world due to the different nature of the place. So they have to figure out how to control their powers again while also helping the RWBY characters in their battles. The RWBY characters could be intrigued by the Persona powers and try to learn from them.