Well, a really interesting plot might involve the Agents of Shield trying to recruit the TMNT for a special mission. Since the turtles have unique skills and knowledge of the sewers and the underbelly of New York, they could be valuable assets. Or perhaps a Kraang invasion occurs in the Agents of Shield universe, and the Agents have to work with the turtles to stop the alien menace. The turtles could teach the Agents some of their ninja fighting techniques while the Agents share their high - tech weaponry and strategies.
A great plot idea could be that some Hydra agents get their hands on a sample of the ooze that created the TMNT. They start creating their own mutant soldiers. The Agents of Shield and the TMNT then have to team up to stop Hydra's mutant army. The turtles' experience with fighting mutants like the Foot Clan would be very useful in this situation. Also, there could be some interesting character interactions, like Fitz trying to understand the turtles' biology or Coulson trying to figure out how to incorporate ninja training into Shield's combat training.
A great plot idea is a crossover centered around a new super - weapon. Maybe some ancient weapon that was lost in the Arrow - verse is found by Hydra in the Agents of Shield world. So the two teams have to work together to retrieve it before it's used for evil. Another popular one is a character - based plot. For instance, if Thea Queen discovers she has some sort of power that is related to the Inhumans in Agents of Shield. She then goes to them for help and that starts a whole series of events that brings the two groups together. Also, a plot where the two teams are forced to compete for a valuable resource, but then realize they need to work together to keep it from falling into the wrong hands can be really interesting.
One really interesting character pairing could be Fitz - Simmons and the TMNT as a whole. Fitz - Simmons are brilliant scientists, and the turtles are a scientific anomaly. They could study the turtles and their mutagenic origin. The turtles could also benefit from Fitz - Simmons' knowledge of advanced technology. Another pairing that would be cool is Agent Ward (assuming he's not evil in this fanfiction) and Leonardo. Ward is a skilled agent, and Leonardo is a skilled ninja. They could exchange fighting and survival skills, and their different perspectives on loyalty and duty could lead to some interesting story arcs.
A mermaid in an Agents of Shield fanfic might also be a victim of some sort of Hydra experiment. They could have been trying to combine the unique physiology of a mermaid with their own technology or powers. This mermaid could then be on the run from Hydra and seek refuge with the Agents of Shield. The agents would then have to protect her while also trying to figure out how to use her abilities to their advantage.
One idea could be that Supergirl's powers are misinterpreted by Shield as a new threat. So they send some of their agents to investigate. The agents then realize she's actually a hero and they team up to fight a common enemy like a powerful alien race that's planning to invade both their worlds.
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.
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.