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.
A powerful ancient artifact is discovered that has the potential to either save the world or destroy it. Both the Agents of SHIELD and the Avengers want to get their hands on it to ensure it's used for good. However, there are also other forces, like Hydra remnants and some alien factions, who are after it too. Skye discovers some ancient writing about the artifact and its powers, which helps the combined team figure out how to protect it. Captain America and Agent Coulson could lead the charge in fighting off the bad guys while Iron Man and Fitz work together to figure out a way to safely store or use the artifact.
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 possible plot could be that Batman somehow gets transported to the world of Agents of Shield. Maybe a strange experiment by Hydra goes wrong and creates a portal. Batman would then use his detective skills to figure out what's going on with all the super - powered and high - tech stuff in the Agents of Shield world. He might team up with Coulson and his team to stop a common enemy, like a new super - villain created by a combination of Gotham's criminal minds and Hydra's evil plans.
Well, perhaps there could be a crossover where a villain from The Flash, say Reverse - Flash, teams up with a Hydra agent from Agents of Shield. This alliance would be a huge shock as they combine their powers and knowledge. Reverse - Flash's speed and ability to manipulate time along with Hydra's devious plans could create a very difficult situation for the heroes from both universes to handle.
One possible plot could be that some of the Agents of Shield end up in the Naruto world through a strange portal. They meet Naruto and his friends and initially have some misunderstandings due to their different cultures and powers. But then they realize they can work together to fight a common enemy, like an organization that is trying to steal both the chakra and the advanced technology from their respective worlds.
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.
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 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.