Well, a great plot could be that there's a new criminal in Gotham who has some sort of speed - based powers, but not as strong as the Flash. Batman realizes he needs the Flash's help to understand how to combat this new foe. Meanwhile, the Flash is dealing with his own issues in Central City like a new speedster gang. When they team up, they discover that the new Gotham villain has ties to the speedster gang in Central City, leading to a big showdown.
One idea could be that the Flash has to help Batman track down a super - villain who has the ability to manipulate time. Since the Flash is a speedster, he can move through time - altered situations more easily. Another plot could involve Batman creating a new gadget to counter a meta - human threat, and the Flash accidentally gets caught in its test run, causing some wacky time - space anomalies that they have to work together to fix.
Perhaps in the fanfiction, a powerful alien entity arrives on Earth and starts causing chaos. It has the ability to phase through matter and move at high speeds. Batman, with his detective skills, figures out a way to track the entity's movements, but needs the Flash's speed to actually catch it. Along the way, they learn more about the alien's motives, which turn out to be related to an ancient Earth artifact. The Flash and Batman must race against time to stop the alien from using the artifact for its evil purposes.
A cool plot might be that a new meta - human emerges who has the power to steal the abilities of other heroes. This meta - human targets the Flash first, leaving him powerless. Batman then has to take the Flash under his wing and train him in more traditional combat skills while they figure out a way to get the Flash's powers back. Along the way, they discover that the mastermind behind this meta - human is an old enemy of Batman who wants to use the Flash's powers to carry out a grand scheme in Gotham.
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.
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.
One idea could be a crossover where The Flash teams up with characters from other CW shows to stop a multiverse - threatening villain. For example, bringing in characters from Arrow to help with their combat skills and strategic planning. Another could be a time - travel plot where The Flash accidentally travels to an alternate version of the CW universe and has to find his way back while dealing with the differences in that world.
In a fanfiction, there could be an alien race that is immune to Supergirl's powers but is vulnerable to the speed force. Flash discovers this during a battle where Supergirl is struggling. He then uses his speed to create a barrier around the aliens, trapping them long enough for Supergirl to figure out a new way to defeat them, like using her super - breath in a new way that Flash helps her direct with his speed.
One idea could be that the Flash and Arrow team up to stop a meta - human who has the ability to control time. They have to race against the clock (literally) to figure out how to neutralize the villain's powers before he rewrites history in a way that destroys Central City and Starling City.
One idea could be that a powerful villain creates a time - space rift that pulls both Supergirl and Flash into an alternate dimension where they have to team up to find a way back home. Their powers work differently in this new dimension, and they have to learn to adapt quickly.
One idea could be that a strange meta - human from The Flash's world somehow ends up in Riverdale. This meta - human has the power to manipulate memories, and starts causing chaos by making the Riverdale characters forget important things about each other. Archie and his friends then team up with Barry Allen to stop this meta - human before their town is torn apart.
One idea could be that the Winchesters are hunting a meta - human in Central City who has powers similar to a demon. The Flash team tries to stop them from killing the meta - human, thinking they are just bad guys. Another could be a time - travel situation where Barry accidentally travels to a world where the Supernatural events are real and has to team up with Sam and Dean to get back home. A third idea is that a powerful witch from the Supernatural universe uses her magic to create chaos in Central City, and the Flash and his friends need the help of the Winchesters to defeat her.
Maybe there's a time - traveling mishap that brings Flash and Supergirl to an alternate universe where their powers are reversed. Flash has to deal with super strength and heat vision, while Supergirl has to learn to control super speed. They must figure out how to get back to their own universes and in the process, they bond over their shared confusion and determination.