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 a story where a new villain emerges who has the ability to manipulate time. The Agents of Shield and the Avengers have to work together to stop this villain before he changes history in a way that destroys the world. Another plot could involve an agent from Shield who discovers a long - lost relative who has superpowers and is being hunted by an evil organization. The agent has to protect their relative while also dealing with the implications of this newfound family member within the context of their work with Shield and the Avengers.
One interesting story could be about how the Avengers react to a particular mission in Agents of Shield that goes wrong. Maybe they step in to help and there are some great character interactions between the two groups.
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.
Another great storyline could be about the Agents of Shield having to deal with the aftermath of an Avengers - level battle. They might be in charge of cleaning up, helping the survivors, and trying to figure out how to prevent such destruction in the future. This could show a different side of the Agents of Shield, as they are often in the background but play a crucial role in the overall Marvel universe.
Another storyline might be a time - travel plot where the agents go back in time to prevent a major event that would have led to the downfall of the Avengers. They could encounter younger versions of the heroes and change the course of history. This would involve a lot of character development and exploring different timelines.
One interesting storyline could be a crossover where Agents of Shield agents have to team up with the Avengers to stop a powerful alien threat that neither group could handle alone. This would involve a lot of character interactions, like Coulson trying to give orders to Iron Man or Natasha Romanoff teaching some of the Shield agents her spy skills.
One idea could be a story where the Agents of Shield team has to team up with some of the less - known Avengers to stop a new, powerful threat that is specifically targeting the more minor superheroes. This would give a chance to explore the dynamics between the two groups and shine a spotlight on the underrated characters.
One idea could be a crossover mission where the Agents of Shield team has to work with the Avengers to stop a powerful alien threat that is targeting both Earth and a hidden Inhuman settlement. The Agents could bring their espionage skills while the Avengers use their raw power.
A fanfic storyline could focus on an alternate universe where the Agents of Shield are not a government - affiliated organization but rather a group of rebels fighting against a tyrannical regime that has taken over the world. They would have to use their skills in a different way and form new alliances.
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.