A fun plot could be that some of the Agents of Shield are actually Squibs or have some latent magical ability that they didn't know about. When they cross paths with the wizarding world through Harry Potter and his friends, they start to discover their magical side. This could lead to a story where they are trained in magic while also using their Shield training to help the wizarding world fight against a new threat, like a group of dark wizards who are trying to create a portal to bring in more powerful dark forces from another dimension.
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 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.
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.
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.
One idea could be that Harry Potter is secretly recruited by SHIELD while still at Hogwarts. He uses his magic to help SHIELD in covert operations against dark wizards who are also involved in muggle - world threats. For example, he could use the invisibility cloak to gather intelligence.
One interesting plot idea could be a new character being introduced who has a special connection to the Shield in the story. Maybe this character has the power to enhance the Shield's abilities and uses it to protect Hogwarts in a different way than expected.