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.
A great plot could be that there's a time - distortion device in Gotham that is affecting both cities. The Flash, being the master of speed, and Batman, with his brilliant detective skills, have to figure out who created it and how to stop it. Along the way, the Flash has to deal with Gotham's dark and narrow streets, which are very different from his own city, while Batman has to understand the science behind the Flash's powers.
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.
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.
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 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.
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.