The story of Captain Carter in the comic often involves her facing unique challenges and using her skills to overcome them. There's a lot of focus on her character development and the alternate universe's impact on her.
Captain Marvel is Carol Danvers. She gained her powers through an interaction with alien technology and has become a powerful hero in the Marvel universe.
One possible plot could be that they meet in an alternate universe where timelines have merged. Captain Carter and Captain America initially have a bit of a misunderstanding as they come from different versions of heroics. But then they realize they share the same values of justice and freedom. They team up to fight a common enemy that is threatening both their worlds, like a powerful time - traveling villain who wants to rewrite history to suit his evil plans.
Red Skull could be the villain. Since he has a long history with Captain America, in a fanfiction where Captain Carter is involved, he could be resurrected or have found a way to cross over from another dimension. He would see Captain Carter as an interesting new threat and Captain America as an old foe to be finally defeated.
One idea could be a story where Captain America and Captain Marvel team up to face a new cosmic threat that's headed towards Earth. They have to combine their unique skills, with Captain America's strategic mind and combat experience on the ground, and Captain Marvel's incredible cosmic powers in space battles.