One interesting plot idea could be Ren traveling back in time to prevent the initial Metaverse incident. This would change the whole course of the story, and he'd have to deal with the consequences of altering such a major event. Maybe he'd face new enemies or form different relationships.
Ren's time - traveling abilities can force him to become more responsible. Since he has the power to change the past and future, he has to think carefully about his actions. Every decision he makes during time travel can have far - reaching consequences, which makes him more cautious and mature.
Perhaps they travel forward in time instead. They could see the consequences of their actions in the future. Maybe they find out that their actions had unintended negative effects on some of their friends or the city as a whole. This would lead them to go back and try to fix things in a different way.
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.
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.
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.
One idea could be a story where the female protagonist and Morgana go on a solo adventure in the Metaverse. They discover a new Palace that no one else has found yet and have to figure out how to take it down together. Another plot could involve Morgana getting lost in the real world and the female character has to find him using her wits and knowledge of his habits. A third idea might be a story where Morgana and the female character share their dreams and aspirations over a late - night conversation in Leblanc.