One possible plot could be that the Avengers are facing an extremely powerful new enemy that they can't seem to defeat. Captain Marvel arrives on Earth just in time. At first, there are some misunderstandings and clashes of egos among the Avengers and Captain Marvel. But as they start to work together, they realize each other's strengths. Captain Marvel's raw power combined with the Avengers' teamwork strategies slowly turn the tide of the battle. Eventually, they defeat the enemy and Captain Marvel decides to stay on Earth for a while to help the Avengers train for future threats.
In a 'Captain Marvel Meet the Avengers' fanfic, there could be an epic showdown against a powerful villain. Captain Marvel's immense power combined with the Avengers' diverse skills would make for an amazing battle. For example, she could team up with Thor to take on an enemy that has the ability to control electricity. Their combined strength of her photon blasts and his lightning strikes would be a sight to behold.
There could also be a story where Captain Marvel has to prove herself to the Avengers. She might be seen as an outsider initially. So she has to show her worth through her actions. She could single - handedly take on a group of powerful villains to gain the Avengers' respect, and then they all work together towards a common goal.
Annihilus could be a likely villain. He is a powerful being from the Negative Zone. In the fanfiction, Annihilus could be drawn to Earth because of the energy signature created when the Avengers and Captain Marvel meet. He sees Earth as a prime target for conquest. His powerful cosmic control rod gives him an edge in battle. The Avengers and Captain Marvel have to quickly learn about his weaknesses and use their combined powers to stop him from destroying Earth and spreading his reign of terror across the universe.
In this fanfic, the main antagonist could be a scientist who has been corrupted by his own experiments. He creates some sort of energy - based monsters that are immune to normal attacks. Captain Marvel and the Avengers have to figure out how to stop these creatures and the mad scientist behind them.
Another fanfiction idea could be a prequel to her role in Avengers: Endgame. It could show what she was doing in the cosmos just before she received the call to return to Earth. Maybe she was facing a different threat that was related to Thanos in some way, and this backstory could add more depth to her character in the movie.
Thanos could still be a likely villain. Even if he was defeated in the official storyline, in a fanfic he could return more powerful or with a new plan. His obsession with the Infinity Stones makes him a great overarching threat.
No, Captain Marvel isn't typically considered the leader of the Avengers in comics. The leadership role often changes among various characters depending on the storylines and events.
Well, in a lot of 'Avengers Captain Marvel fanfiction', Loki can be a very interesting character. His mischievous nature can lead to all sorts of plot twists when interacting with Captain Marvel. Scarlet Witch is also popular, as her powers and Captain Marvel's can have some really cool and unexpected interactions, whether they are on the same side or opposing each other.