Perhaps there could be a time - travel related plot. A device is accidentally activated in a S.H.I.E.L.D. lab that sends some Agents and Avengers back in time. They end up in a crucial moment in history, like during World War II. There, they meet younger versions of some of the Avengers. They have to work together without changing the timeline too much while also finding a way back to their own time.
I think the interaction between Bruce Banner and Fitz - Simmons would be fascinating. Fitz - Simmons are brilliant scientists, and Banner is a scientific genius himself. They could collaborate on some new scientific research, like finding a way to control the Hulk better or developing new energy sources. Also, Clint Barton and Skye could have an interesting dynamic. Clint's no - nonsense approach and Skye's hacker - turned - agent background would make for some great banter and teamwork.
A mermaid in an Agents of Shield fanfic might also be a victim of some sort of Hydra experiment. They could have been trying to combine the unique physiology of a mermaid with their own technology or powers. This mermaid could then be on the run from Hydra and seek refuge with the Agents of Shield. The agents would then have to protect her while also trying to figure out how to use her abilities to their advantage.
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.
Well, the plot could involve the Agents of Shield having to team up with the Avengers to stop a common enemy. Maybe a powerful alien threat or a super - powered villain that neither group can handle alone. The Agents could bring their espionage and covert ops skills, while the Avengers contribute their raw power.
A great fanfic idea could be about an old enemy from the Agents of Shield's past coming back and the Avengers being brought in to help. It could involve a lot of mystery, action, and the building of new relationships between the two groups.
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.
Definitely Captain America. His strong sense of justice and leadership makes him a great character to build a story around. Also, Agent Coulson is really popular. Fans love his dry humor and his ability to hold his own against super - powered individuals. And then there's Black Widow. Her mysterious past and badass fighting skills are always interesting to explore in fanfiction.