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.
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.
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 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.
One idea could be that the Avengers need the Agents of Shield's help to track down a new, powerful and elusive villain who has technology that can disrupt the Avengers' powers. The Agents use their espionage skills to gather intel while the Avengers provide the muscle when it comes to confronting the bad guy.
One idea could be that some of the Agents of SHIELD team get transported to Starling City where they cross paths with Arrow's team. They could team up to fight a common enemy like a meta - human terrorist group that has access to both high - tech weapons and ancient magic.
One idea could be that the Agents of Shield discover a new group of Inhumans with a unique power that could be a threat or an asset. They have to decide whether to help them control their powers or contain them. Another could be an Inhuman from the Inhumans group joins the Agents of Shield to help fight a common enemy, like a new alien threat. And a third idea is that some technology from Agents of Shield accidentally causes a power surge among the Inhumans, leading to chaos that both groups must work together to resolve.
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.