If Barry kidnapped Supergirl in fanfiction, it could be a really interesting plot twist. Maybe Barry has been affected by some sort of red kryptonite - like substance that makes him act out of character. This would lead to a conflict between the Flash and Supergirl's friends and allies. They would be confused as to why Barry would do such a thing.
One of the best places to find Flash and Supergirl fanfiction is Archive of Our Own (AO3). It has a large collection of fan - created stories that cover all kinds of scenarios and relationships between the two characters. The site is well - organized, making it easy to search for specific tags or themes related to Flash and Supergirl.
One great Flash and Supergirl fanfiction is 'The Team -Up of Legends'. It shows an alternate universe where they have to work together against a powerful new villain. The story does a great job of portraying their different powers and how they complement each other in battle.
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.
Another possibility is that Barry was kidnapped himself first and then forced to kidnap Supergirl. The real kidnappers could be a group of meta - humans who want to create chaos by pitting two of the most powerful heroes against each other. Barry would be in a difficult situation, having to do something against his will, and Supergirl would initially be confused and angry at Barry until they both figure out what's really going on.
Well, Cisco Ramon from The Flash would be a great addition. He could use his tech skills to create some new gadgets or figure out ways to counter the villains' powers. Also, Martian Manhunter from Supergirl's side. His shape - shifting and telepathic abilities would add a whole new dimension to the story.
In a fanfiction scenario where Barry is stabbed during a Flash - Supergirl crossover, it could lead to a lot of interesting plot developments. Maybe Supergirl would have to step up and use her powers in new ways to protect Central City in Barry's absence. She might have to team up with the other members of Team Flash more closely.
One interesting storyline could be a team - up against a powerful new villain that neither The Flash nor Supergirl can defeat alone. They have to combine their powers and strategies in a way they've never done before.
The plot could involve a mind - control situation. Some villain tries to control Supergirl, but Flash manages to break the control. In the process, they have a deep emotional connection and kiss. This would show Flash's heroism and how it affects their relationship.