The Riddler could be a great main antagonist. He could create puzzles and traps that are based on both the Flash's speed and Gotham's dark secrets. For example, he might set up a trap where the Flash has to run through a maze of moving walls in Gotham while also solving riddles that are related to Batman's past.
A new meta - human villain created specifically for the crossover could be interesting. This villain could have the power to control shadows and use them to move quickly, mimicking the Flash's speed in a way. In Gotham, he could use the city's many dark corners and alleys to his advantage. He could also be a master of disguise, fooling both the Flash and Batman. His motives could be to take over both Gotham and Central City and create a new world order where meta - humans rule over normal humans.
In a Gotham Flash crossover fanfiction, perhaps there's a device that disrupts the speed force and it's located in Gotham. The Flash has to go there to fix it. He meets the various characters in Gotham like the Joker, who tries to use the Flash's powers for his own chaos. Meanwhile, Flash has to work with the likes of Gordon and Robin to stop the Joker and repair the device. The different moral compasses of the Gothamites and the Flash could lead to some interesting character interactions.
Perhaps there's a villain in Gotham who has discovered a way to siphon the Flash's speed force. The Flash has to go to Gotham to stop this villain, and in the process, he meets the various characters of Gotham like Gordon and Catwoman. They all have to work together to not only stop the villain from stealing the speed force but also from using it for some evil plan in Gotham.
Flash crossover fanfiction is fan - created stories that combine elements from the 'Flash' (a superhero character or related media) with elements from other fictional universes. For example, it could be a story where The Flash meets characters from the 'Harry Potter' series and they have an adventure together. It allows fans to explore new and exciting scenarios that the original creators might not have thought of.
The plot should be engaging and make sense. It can't just be a random mash - up. A good Gotham crossover fanfiction will have a plot that ties the two (or more) universes together in a logical way. Maybe there's a common threat that forces the characters to work together, like a super - villain that exists in both universes and the characters from Gotham and the other crossover property have to find a way to stop it.
It could be amazing. Imagine Clark Kent from Smallville finding himself in the dark and gritty Gotham. He might use his powers to help Batman clean up the city in a different way. Their different moral compasses could lead to some interesting interactions, like Clark's more idealistic view clashing with Batman's darker pragmatism.
I think in 'Marvel The Flash Crossover Fanfiction', the most interesting part would be how the Flash's abilities are perceived in the Marvel universe. Since the power scales and the overall feel of the two universes are different. Maybe the Flash would be seen as an anomaly, or perhaps a new kind of hero that the Marvel characters have to adapt to. It could also explore how the Flash's speed affects time and space in a world that already has characters like Doctor Strange who are well - versed in such concepts.
One idea could be that a powerful villain threatens both their cities simultaneously. Supergirl and The Flash have to team up, and in the fanfiction, their different powers and personalities could lead to some interesting interactions. For example, Supergirl's strength and The Flash's speed could be combined in unique ways to defeat the villain.
One possible plot could be Naruto being transported to Gotham. He might initially be confused by the dark and crime - ridden city. But with his ninja skills, he could start to fight crime in his own unique way, perhaps using his shadow clones to patrol different areas of Gotham simultaneously. His positive and determined attitude could also inspire some of the more down - trodden citizens of Gotham, like the orphans in the city.