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 idea could be that Supergirl's powers are misinterpreted by Shield as a new threat. So they send some of their agents to investigate. The agents then realize she's actually a hero and they team up to fight a common enemy like a powerful alien race that's planning to invade both their worlds.
In this Naruto and Supergirl crossover, Naruto is on a mission in a strange new world and suddenly meets Supergirl. They initially misunderstand each other as threats. But as they start to communicate, they realize they both have a strong sense of justice. They team up to stop a powerful villain who is using a mix of ninja and Kryptonian technology to wreak havoc. Naruto uses his shadow clones and rasengan, while Supergirl uses her heat vision and super strength to take on the baddie.
First, you need to understand the characters well. For Supergirl, know her powers, her moral code, and her relationships. For Agents of Shield characters, like Coulson, Daisy, etc., study their personalities and abilities. Then, create a believable scenario for their meeting. It could be something like a shared threat or an accident that brings them together.
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 great Supergirl crossover fanfiction is 'Supergirl and the Flash: Worlds Collide'. It has an exciting plot where Supergirl and the Flash team up to face a common enemy that can manipulate time and space. The story does a great job of capturing the essence of both characters and their unique powers.
A really interesting plot could be a time - traveling crossover. Supergirl goes back in time to the era of the original Avengers. She helps them in a battle that changes the course of history. In return, the Avengers help her find a way back to her own universe. During this time, she forms a special bond with Thor, as they both have superhuman strength and a connection to otherworldly powers.
Well, one possible plot could be that Supergirl accidentally lands in the Naruto universe. Naruto, being the curious and friendly ninja he is, approaches her. They initially have a misunderstanding due to their different worlds and powers, but then they realize they can learn from each other. Supergirl could teach Naruto about her advanced technology from her world, while Naruto could show Supergirl the unique chakra - based powers and the ninja way of life.
A great moment could be when they first meet and realize how different yet similar their worlds are. Supergirl might be in awe of The Flash's speed, and The Flash could be impressed by Supergirl's strength. It's a moment of mutual respect that often sets the tone for the rest of the story.
Another theme is the power struggle. Smallville often focused on Clark's journey to control his powers, and Supergirl has her own power - related challenges. In crossovers, they might face a common enemy where their combined powers are needed, and this creates a power struggle dynamic as they figure out how to work together effectively.