An original character could be the main antagonist. For example, a powerful alien sorcerer who has the ability to drain the powers of superheroes. He targets the Avengers and Captain Marvel specifically because of their combined strength, and they have to find a way to stop him before they all lose their powers.
Ultron could be reimagined as an even more advanced and dangerous version in the fanfic. He could have developed new ways to infiltrate the Avengers' defenses and has a vendetta against Captain Marvel for interfering in his previous plans. The fight against this upgraded Ultron would be intense and require all of their skills and teamwork.
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.
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.
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.
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.
An alien race with a grudge against the Republic could also be the main antagonist. They might target Rex specifically because of his strategic importance and his role in leading many successful missions against them in the past. His death at their hands would be a major blow to the Republic's morale.
Loki could be a great main antagonist. He could be the mischievous student who's always causing trouble for the Avengers. He might use his magic to play pranks on them or steal their homework to make them look bad in front of the teachers.
A new, original villain created just for this fanfic could be the main antagonist. This villain could be a powerful sorcerer who has been observing the Avengers from the shadows. When the OC is reborn, they sense a disruption in the magical balance of the world. Believing the OC to be a threat to their own plans of ruling the world through magic, they set out to eliminate the OC and in the process, come into conflict with the Avengers.
Loki could also be a main antagonist. He could see Ben as an interesting new player in the universe and try to manipulate him for his own gain. Or he might want to use the Omnitrix to cause chaos across the multiverse.
She could meet a very smart science teacher who is intrigued by her powers and wants to study them scientifically.
The main antagonist could be a powerful sorcerer. As I mentioned before, in the context of a magical curse causing the weight gain. This sorcerer could have his own motives, like trying to take over the world by first weakening the Avengers' most iconic figure. He could use his dark magic to mess with Captain America's body and make him gain weight, and then use this as a distraction while he executes the rest of his evil plan.