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.
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.
In some fanfiction, there could be crossovers with other Marvel properties. For instance, the Agents of Shield team could meet the X - Men. This would create a whole new set of dynamics and story possibilities. They might have to work together to stop a mutant - hating villain who is also after SHIELD secrets. Another idea could be a story where they encounter Doctor Strange and have to deal with a magical threat that they are completely unprepared for.
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 interesting storyline could be Skye's struggle to communicate while being mute within the context of the team's missions. For example, she might develop a unique form of sign language that only the team members gradually learn to understand, which could add a new layer of teamwork and bonding. Another could be how she uses her hacking skills in a different way since she can't verbally interact as easily, perhaps finding ways to leave digital messages that are only decipherable by certain members of the team.
One idea could be a fanfic where Miles has a secret power that he discovers while on a mission with the Agents of Shield. This power could be something that changes the dynamic of the team and how they operate.
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 of my favorite storylines is the Framework arc. It was so interesting to see the alternate reality where Hydra ruled. The characters were different yet still recognizable, and it was exciting to see how they broke free from that false world.
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 plot twist could be that the lie detector is actually malfunctioning but gives correct results in a completely random and unexpected way. For example, it might say someone is lying when they're actually telling the truth about a minor detail, but that minor detail leads to a major discovery. Another twist could be that the person operating the lie detector has an ulterior motive and is manipulating the results to frame someone. They could be using it as a tool to further their own secret agenda within S.H.I.E.L.D.