Maybe a virus is spreading that targets superhumans. The Avengers start getting affected one by one. The Agents of SHIELD, being more used to dealing with biological threats, step in. Daisy could use her quake powers to contain the virus in certain areas. May could train some of the Avengers in hand - to - hand combat techniques they might be lacking. And together, they search for the origin of the virus, which turns out to be an experiment gone wrong in a hidden SHIELD facility from the past. They then have to race against time to find a cure before all the superhumans are wiped out.
In Avengers fanfiction, Phil Coulson is often considered one of the best Shield agents. He is highly dedicated, intelligent, and has a deep understanding of the Avengers. Another great one could be Maria Hill. She is tough, strategic, and can handle high - pressure situations well. And then there's Clint Barton, who combines his excellent archery skills with his Shield agent training.
One idea could be that the Agents of Shield discover a hidden threat that is related to an old Avengers enemy. For example, a Hydra remnant has found a way to re - activate some of the technology left behind by Ultron. The Agents of Shield then have to team up with the Avengers to stop this new threat. They could combine their skills, like the Agents' espionage and the Avengers' super - powers.
One idea could be that the Agents of Shield discover a new threat that is related to an old enemy of the Avengers. They have to team up to figure out how to stop it. For example, a hidden Hydra cell has found a way to re - activate an old weapon that was once used against the Avengers.
Perhaps a virus is released that targets enhanced individuals. The Avengers are directly affected, but the Agents of Shield has some research on a similar virus from a previous mission. They team up to find a cure. Along the way, they face off against a group of mercenaries who are trying to use the chaos to steal valuable technology from both the Avengers and Agents of Shield.
I think Natasha Romanoff and Melinda May would be an interesting pair. Both are strong, badass women with a lot of combat experience. They could share their stories of their past missions, and also train together. Maybe they could even have a friendly competition to see who is better at hand - to - hand combat or espionage.
I think Daisy Johnson would be really interesting. She has her unique powers and a complex backstory from her time in SHIELD. In a crossover, she could interact with the likes of Thor. Maybe she could learn some new ways to control her powers from him, as he has experience with his own godly powers. And she could also show the Avengers her skills in combat and stealth that she learned in SHIELD. It would be fascinating to see how she holds her own among the super - powerful Avengers.
I think the interaction between Coulson and Captain America would be really interesting. Coulson is a big fan of Captain America, and Steve would be impressed by Coulson's leadership and the way he holds his team together. They could exchange stories about their different experiences in the war - Steve from World War II and Coulson from more modern conflicts.
Definitely Captain America and Agent Coulson. Captain America represents the old - school heroism of the Avengers and Coulson is the heart and soul of Agents of Shield. Their different leadership styles and moral compasses would create a great dynamic. They could learn from each other, like Coulson teaching Cap about modern technology and Cap teaching Coulson about the values of the past.
One idea could be that Supergirl's powers are misinterpreted by Shield as a new threat. So they send some of their agents to investigate. The agents then realize she's actually a hero and they team up to fight a common enemy like a powerful alien race that's planning to invade both their worlds.