Well, a cool plot might be that the Naruto characters somehow get transported to the Agents of Shield universe. Naruto, with his positive attitude, would befriend the agents quickly. They could team up to stop a powerful villain who is using a combination of ninjutsu-like powers and advanced weaponry. For example, the villain could be creating clones using some sort of high - tech device inspired by the Shadow Clone Jutsu, and they have to figure out how to stop him.
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.
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.
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.
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.
The plot of such a fanfiction could revolve around a mystery that combines the two universes. There could be a villain who wants to steal Wonka's secret recipes and use them for evil purposes, and the Agents of Shield are the only ones who can stop it. They'd have to navigate the sweet yet dangerous world of Wonka's factory, facing off against the villain's minions while also trying not to get distracted by all the delicious treats. It would be a story full of action, humor, and a touch of magic.
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.
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.