One idea could be a crossover with the Doctor from Doctor Who. The Doctor could land in National City and team up with Supergirl to fight an alien threat that's beyond the capabilities of either of them alone. Maybe it's an enemy that can manipulate time, which is where the Doctor's expertise comes in handy.
A 'Avengers Supergirl Crossover Fanfiction' might involve Supergirl's Kryptonian powers being a mystery to the Avengers at first. She could show off her super strength, heat vision, and flight, and the Avengers would be in awe. Then they'd start to strategize together. For example, Captain America would lead the group with his military tactics, while Supergirl uses her powers to do the heavy - hitting. And Hulk and Supergirl could have a fun interaction comparing their strength.
Another theme is the exploration of different universes. Sometimes the fanfictions will send the characters into alternate realities where they have to adapt and find their way back. This allows for a lot of creativity in terms of world - building and character development. Also, friendship is often a key theme. These heroes come from different shows but in the crossovers, they form strong bonds and support each other through tough situations.
Mr. Schuester from Glee could be a main character too. He could be the one who tries to bring the two groups together, seeing the potential in the Glee club and Supergirl working as a team. His role as a mentor in Glee could be extended to Supergirl as she tries to navigate the more complex aspects of human relationships and teamwork in this crossover fanfiction.
One idea could be that the Glee club is invited to perform at a big event in National City where Supergirl is also present. They could end up teaming up to save the day when an alien threat targets the event. The Glee kids' unique talents could be used in unexpected ways, like using their voices to disrupt an alien's sonic weapon.
Well, it could be about Supergirl getting accidentally transported to the Marvel universe. She might team up with Captain Marvel. They could fight a common enemy like Thanos who has somehow gotten his hands on Kryptonian technology. It would be a clash of two very different power sets and universes.
Perhaps in this fanfiction, Barry's death causes a rift in the multiverse. Supergirl then has to team up with other heroes from different universes to try and fix it. His death could be the start of a much larger threat that only a united front of heroes can face. She might struggle with the guilt of not being able to save him at first but then turns that into motivation.
One possible plot could be that Supergirl, through some sort of inter - dimensional rift, ends up in the Star Wars universe. She might team up with the Rebel Alliance. Her superpowers would be a great asset against the Empire. For example, she could easily take down Imperial starships with her heat vision or super strength. Maybe she'd have to learn to use a lightsaber too, which would be an interesting addition to her powerset.
One popular storyline is when Flash and Supergirl team up to fight a common enemy from another dimension. This allows for a lot of action and showcases their different powers working together.
First, decide which universe or character you want to crossover with. For example, if it's with Star Trek, think about how the two different settings can interact. Then, create a plot. It could start with Supergirl being pulled into the Star Trek universe by some sort of spatial anomaly. After that, develop the characters' reactions to each other. How would Captain Kirk react to Supergirl's powers? Just start writing and let the ideas flow.