Maybe there's a time - traveling aspect to the crossover. The Flash accidentally travels back in time to Gotham in the past. He meets a young Bruce Wayne before he becomes Batman. The Flash has to help Bruce deal with some early villains in Gotham while also trying to find his way back to his own time. This could involve Flash teaching Bruce some things about speed and movement, which later influence how Batman moves and fights, and Bruce in turn shows Flash how to be more stealthy in a city full of danger.
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.
Maybe there's a meta - human or a super - villain who is causing chaos in both cities. Batman is too occupied with Gotham's internal affairs, so Arrow comes to help. They discover that the villain has a base in an abandoned area between the two cities. They have to combine their resources, like Arrow's high - tech arrows and Batman's detective skills (even if Batman himself isn't directly involved but his influence on Gotham's crime - fighting is there), to take down the bad guy.
A Reverse Flash crossover with the Flashpoint timeline could also be great. The Reverse Flash could try to further manipulate the already - altered Flashpoint world. This could involve him trying to turn heroes into villains and vice versa, causing chaos in a world that is already on the brink of collapse.
One idea could be that the characters from Glee find themselves in Central City during one of The Flash's battles. Maybe they get caught in the crossfire and The Flash has to save them while also dealing with the meta - human threat. For example, Rachel could be singing on the street when a meta - human causes chaos nearby.
A cool concept for twilight and flash crossover fanfiction could be a time - travel aspect. What if a character from The Flash travels back in time and accidentally alters the history of the Twilight world? This could lead to all sorts of chaos, like vampires ruling the world instead of just being in hiding. Or, a Twilight character could use the Flash's speed - related technology to gain an edge in their own battles, like using it to quickly escape from a werewolf pack.
Another concept is that a villain from The Flash's world uses the power of music (inspired by the Glee club's performances) to create chaos. The Flash teams up with the Glee club to reverse the effects of the music - based villainy. The Glee kids could use their knowledge of harmony and rhythm to counter the negative musical energy, while the Flash uses his speed to stop the physical manifestations of the villain's attacks.
One idea could be a crossover with the Teen Titans. Kid Flash could team up with them to fight a new super - villain that is causing chaos across multiple cities. His speed could add a new dynamic to the Titans' combat strategies.
One idea could be a crossover with another superhero show where The Flash has to team up with their heroes to stop a multiverse - threatening villain. Maybe he teams up with Arrow and they have to combine their skills to take on a speedster from another dimension who can also turn invisible.
Well, perhaps there could be a plot where a character from The Flash, like Barry Allen, discovers the existence of the Twilight world. He might be intrigued by the vampires' powers and try to study them in a scientific way. Meanwhile, the vampires in Twilight might see Barry as a threat or an opportunity. For example, they could try to use his speed for their own purposes, like hunting more efficiently. This could lead to a complex relationship between the two universes.
A plot could involve the Avengers trying to understand the Flash's powers. Tony Stark might be especially intrigued and try to create technology to mimic the speed force. Meanwhile, the Flash could be in awe of the Avengers' different abilities and learn new ways to use his speed from them. For example, he could learn combat strategies from Captain America or how to better control his powers from Doctor Strange. And then they all have to face a threat that only their combined powers can defeat, like a cosmic entity that is draining the life force of both their universes.