A cool plot could involve the Persona 5 crew going back in time to the events of Persona 3. They might end up interfering with some of the original events, which could have unforeseen consequences. For example, they could accidentally change the way a key character in Persona 3 awakens their Persona, and then have to figure out how to fix it while also dealing with the Shadows in that era.
Another option is a crossover with the Pokémon world. The Phantom Thieves could travel to a region in the Pokémon world and discover that someone is using Persona powers to make Pokémon act out of control. They would need to catch Pokémon themselves and use their combined powers of Personas and Pokémon to stop the bad guy. It would be interesting to see how they interact with Pokémon trainers and the whole Pokémon ecosystem.
One idea could be to cross it with another popular RPG. For example, having the Persona 4 characters enter the world of Final Fantasy. They could interact with the different races and magic systems there. Another could be a crossover with a detective - themed anime. The Investigation Team could team up with the detectives from that anime to solve a mystery that spans both worlds.
A great plot could involve the transfer of Personas between the two groups. For example, a character from Persona 3 accidentally gets a Persona that belongs in the world of Persona 4 and vice versa. This causes chaos as they have to learn to control and understand these new entities while also dealing with the reactions of their respective teams.
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 that the RWBY characters enter the Metaverse from Persona. They might have to face their Shadows, which could be related to their Grimm - fighting fears or personal insecurities. For example, Ruby could face a Shadow that represents her fear of not being able to protect everyone.
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.