One idea could be that Flash and Supergirl team up to stop a powerful alien villain who is causing chaos across both their cities. The villain could have the ability to manipulate time and space, which would make it a real challenge for the two heroes.
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 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.
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.
One idea could be that a powerful villain from another dimension is trying to take over all three of their cities simultaneously. The Supergirl, Flash and Arrow have to team up, each using their unique abilities. Supergirl could use her super strength to take on the villain head - on, Flash could use his speed to disrupt the villain's plans and steal important items, and Arrow could use his archery skills to set up traps and distractions.
One idea could be that a powerful villain from another dimension is causing chaos in both Supergirl's and the Flash's cities. They have to team up, with Supergirl using her strength and flight to combat the villain's minions on a large scale, while the Flash uses his speed to disrupt the villain's energy sources. Maybe they also discover a connection between their powers that helps them defeat the villain in the end.
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 plot idea could be that a character from Flash, like Barry Allen, somehow gets zapped into the Glee universe. He could be confused by all the singing and dancing at first, but then use his speed to help the Glee club prepare for a big competition in a very short time. For example, he could quickly gather all the necessary props or help the members with their choreography by demonstrating moves at super - speed.
One idea could be that a supernatural entity from the Supernatural world somehow ends up in Central City and starts causing chaos that only the Flash's speed can help contain. For example, a demon that can possess multiple people at once and the Flash has to use his speed to track down all the possessed bodies before the demon can complete a dark ritual.
In this fanfiction, The Flash and Supergirl could start off as rivals. They both think their way of protecting people is the best. But as they face a common enemy that is too strong for either of them alone, they learn to work together and respect each other's abilities.
In this fanfic, the plot could be really interesting. Since it's a crossover, there could be a unique blend of the Supergirl and Flash universes. Kara's pregnancy might be a catalyst for a big change in the story. For example, it could lead to a new form of power or ability within Kara that is related to motherhood. Flash could be the one to first notice the changes in Kara's powers because of his quick thinking and observational skills. The story might also involve a race against time as they try to protect Kara and the unborn baby from a villain who wants to use the baby's potential powers for evil purposes.