A plot where Supergirl's powers are somehow linked to the Infinity Stones could be really cool. The Avengers need to figure out how to use her powers in relation to the Stones to defeat an enemy who is also after the Stones' power. This would create a complex and exciting story with lots of action and mystery.
Maybe a story where the Avengers are transported to Supergirl's universe. They have to adapt to her world's rules and help her fight against a powerful villain there. This could involve a lot of world - building and character development as the Avengers learn about Supergirl's allies and enemies.
One idea could be that Batman and Supergirl team up to stop a powerful alien threat that is beyond the capabilities of either of them alone. They start off distrusting each other due to their different methods, but as they face challenges, they learn to work together and respect one another's skills.
One idea could be exploring what if Loki had an unexpected ally within the Avengers. Maybe a character who was initially on the heroes' side but got swayed by Loki's charm or promises.
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.
One plot idea could be that the Inhumans' city of Attilan is in danger and the Avengers are called in to help. The Inhumans are initially hesitant to accept their aid due to their differences, but they soon realize they need to work together. Another idea is a young Inhuman with a powerful but uncontrollable ability is found by the Avengers. They try to help the Inhuman learn to control it while also protecting them from those who would use their power for evil.
A more complex plot could involve the Flash's speed force interacting with the Infinity Stones. The Avengers might be trying to figure out how to use or contain the power of the speed force in relation to the Stones. This could lead to all kinds of conflicts and alliances within the story, as different characters have different ideas about how to handle such a powerful and unknown combination of forces.
A plot could revolve around the Avengers Prime traveling through time to prevent a future disaster that they somehow caused. Along the way, they meet different versions of themselves and have to make tough decisions about changing the timeline.
One could be a Supergirl fanfic about her teaming up with other superheroes from different universes to fight a powerful cosmic villain. It would involve epic battles and interesting character interactions.
A really interesting plot could involve the Tesseract from the Avengers. It could be that the Tesseract has some sort of connection to the Darkness in SPN. When the Avengers are trying to protect the Tesseract, they accidentally release some of the Darkness. The Winchesters, with their knowledge of the supernatural, and the Avengers, with their superpowers, must then join forces to contain the Darkness again. The characters could also have some really fun interactions, like Dean being in awe of Iron Man's technology and Steve Rogers being impressed with Sam and Dean's hunting skills.
One idea could be a story where a new villain emerges who has the ability to manipulate time. The Agents of Shield and the Avengers have to work together to stop this villain before he changes history in a way that destroys the world. Another plot could involve an agent from Shield who discovers a long - lost relative who has superpowers and is being hunted by an evil organization. The agent has to protect their relative while also dealing with the implications of this newfound family member within the context of their work with Shield and the Avengers.
One plot idea could be that a powerful Pokemon is corrupted by an Infinity Stone - like object. The Avengers, who are familiar with the power of the Stones, team up with the Pokemon Champions to purify the Pokemon. The Champions know how to communicate with Pokemon on a deeper level, which helps in the process.