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.
Thanos could still be a great antagonist even in a fanfic. He could come back with a new plan to obtain the Infinity Stones again. His powerful and menacing presence would create a high - stakes situation for Captain Marvel and the Avengers to face.
It could be a powerful alien warlord who has set his sights on Earth. This antagonist might have an army of powerful minions and technology that rivals Captain Marvel's and the Avengers' combined powers.
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.
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.
There's a possibility that it's an old enemy of the Avengers who sees this as an opportunity. For example, Hydra could be involved. They might try to manipulate the situation to bring down both the rogue avengers and Peter Parker. They could spread false information to make the public turn against them all, while they carry out their own evil plans in the shadows.
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.
She could meet a very smart science teacher who is intrigued by her powers and wants to study them scientifically.
It could be Hydra. They might be trying to take advantage of the split between the Avengers and the Rogue Avengers. They see Peter as a wild card and try to either capture or turn him against both groups.
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.