One idea could be to cross Supreme Commander with a sci - fi RPG like Mass Effect. The Supreme Commander's advanced technology could be introduced into the Mass Effect universe, causing a stir among the various species. Maybe the protagonist has to figure out how to use the Supreme Commander's strategic resources to fend off a new Reaper threat.
Another plot could involve a crossover with Star Wars. Picture the huge mechs from Supreme Commander on the battlefields of Star Wars. The Galactic Empire or the Rebel Alliance might try to either commandeer or destroy these powerful machines. It could lead to some really epic space and ground battles.
A plot could revolve around a character from Starcraft 2 who gets transported to the world of Supreme Commander. Let's say a Terran marine finds himself in the middle of a Supreme Commander battlefield. He has to figure out how to survive and get back home. Along the way, he teams up with some of the commanders in Supreme Commander and learns about their strategies. He then tries to adapt his own combat skills from Starcraft 2 to this new environment. This could include things like using his rifle in different ways or learning to communicate with the more robotic - like units in Supreme Commander.
One idea could be exploring the backstory of the dragon commanders. Maybe how they were chosen and trained before they took on their important roles. Another could be a story where a dragon commander has to form an alliance with an unexpected group to save their land from a new, powerful threat.
One interesting concept could be the combination of the strategic gameplay elements from Supreme Commander with the rich sci - fi universe of Halo. For example, how the different factions in Supreme Commander might interact with the Covenant or UNSC in Halo. Maybe the advanced technology in Supreme Commander like the huge mechs could be integrated into the Halo battles, creating new and exciting combat scenarios.
One interesting plot idea could be Thorn being transported to a different era in the Star Wars universe through some sort of time - warp anomaly. He could then have to team up with unlikely allies to get back to his own time. Another idea is that Thorn could cross over into a parallel Star Wars universe where the rules are slightly different and he has to adapt quickly. Maybe he finds himself in a universe where the Sith are in control and he has to lead a rebellion.
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.
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.
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.
Another plot could involve a crossover with the Punisher and the X - Men. Frank Castle might find himself in a situation where he has to work with mutants. He could initially be distrustful but then realize they are fighting for a similar cause against a common enemy that is targeting both humans and mutants. For example, a group of anti - mutant and anti - vigilante fanatics.
One idea could be a crossover with Peter Pan. Tinkerbell could meet characters from another world, like Alice from Wonderland. She might be confused by the strange rules and creatures there, and her magic could interact in unexpected ways with the Wonderland magic.
Another plot could involve a crossover with a post - apocalyptic world. The Boys find themselves in a world where society has collapsed, and they have to team up with the survivors against new threats. This could bring out new sides of the characters as they are forced to adapt to a completely different environment and face challenges they've never faced before.