A time - traveling criminal could be the main villain. He has altered the past to create a future where he rules the world. Flash has to track him through different time periods, deal with the changes he has made, and ultimately defeat him to restore the correct timeline.
It could be a speedster from another universe who has come to challenge Flash. This villain might have some unique powers related to speed that Flash has never encountered before, like the ability to steal speed from other objects or people.
The Reverse - Flash could be a great main villain. He could travel to Gotham to cause chaos and draw out the Flash. His time - manipulation abilities would pose a huge threat not only to the Flash but also to Batman's carefully planned strategies in Gotham. Batman would have to adapt to dealing with a villain who can move at super - speed and mess with time.
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.
It could be about Flash exploring a new dimension. Maybe he stumbles upon a world where the laws of physics are different, and he has to use his super - speed in creative ways to survive and find his way back home.
Maybe a new character, an ancient sorcerer who was once banished and now wants to use the Red Throne as a means to regain his power and take over Ooo. He could be a mysterious and powerful foe.
It could be a powerful and corrupted Digimon that has the ability to manipulate the digital boundaries. This Digimon could be from a region that was previously unknown in both the Adventure and Frontier worlds. It wants to merge all the digital worlds into one chaotic realm where it can rule supreme.
It could be a new, previously unheard - of ninja who has the potential to become as great as the Yellow Flash. Maybe a young orphan who discovers some hidden power within themselves.
In a new Ash Unova fanfiction, the main villain could be a scientist who is conducting unethical experiments on Unova Pokémon. He believes that by fusing different Pokémon together, he can create the ultimate Pokémon. His experiments are causing harm to the Pokémon involved and are also disrupting the natural balance in the Unova region. Ash discovers what's going on and has to stop the scientist, not only to protect the Pokémon but also to save the Unova region from the potential disasters that could be caused by these abnormal Pokémon creations.
Perhaps an interdimensional villain. This villain could be causing disruptions in both The Flash's and Supergirl's dimensions, forcing them to meet and join forces to stop it. The villain could have powers that are a challenge for both of their unique abilities.
The Reverse Flash could also be a main villain in this crossover. He travels to the Smallville universe to cause trouble. He might target Clark, thinking that by eliminating him early, he can change the future in his favor. This would force Barry and Clark to work together to stop the Reverse Flash's evil plans.
A powerful wizard from a forgotten dimension could be the new villain. He sees Seabrook as a place full of unique energy that he can use to gain more power. He starts by creating chaos among the zombies, aliens, and humans, using his magic to turn them against each other.