A plot could involve a time - traveling anomaly that brings an evil version of themselves from the future. They must figure out how to send these evil counterparts back while also dealing with the chaos the time - travel has caused in their present. For example, it could have merged parts of their cities together or caused some people to have strange powers. They would need to work together, with Flash's knowledge of time travel, Supergirl's ability to handle powerful threats, and Arrow's strategic thinking.
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.
Well, a great plot for Supergirl Arrow crossover fanfiction could be centered around a common enemy from another dimension. This enemy has technology that nullifies Supergirl's powers and Arrow's skills, so they have to rely on their wits and each other's unique strengths. For example, Supergirl could use her heat vision in a creative way to expose the enemy's weaknesses while Arrow uses his archery skills to set up distractions. They could also meet some interesting characters from the other dimension during their adventure.
One idea could be that an alien threat emerges which requires the skills of both Arrow's team in Star City and Supergirl in National City. They have to combine their combat styles, with Arrow's more grounded and stealthy approach and Supergirl's super - powered attacks. For example, Arrow could use his trick arrows to create distractions while Supergirl takes on the stronger alien foes directly.
One idea could be that a powerful villain threatens both Star City and National City simultaneously. Arrow and his team are struggling with the more street - level threats in Star City, while Supergirl is dealing with the super - powered aspects in National City. Eventually, they cross paths when the villain's plan connects the two cities. For example, the villain might be using some sort of technology that is affecting the meta - humans in National City and also causing chaos in Star City's criminal underworld.
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 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.
Maybe there could be a crossover where the Flash accidentally travels to the Arrow's universe and they have to work together to get him back to his own world. Along the way, they discover a common enemy that has been operating in both universes.
A plot twist could be that a character from one of the shows, who seems to be a minor or unassuming figure, is actually a powerful being from the future sent to manipulate the events of the crossover. This person has been subtly guiding the actions of the heroes, and when the truth is revealed, it completely changes the heroes' perception of the events they've been through and who they can trust.
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.