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 exciting plot twist could be the discovery of a hidden connection between Smallville's Clark Kent and The Flash's Barry Allen that predates their superhero identities. Maybe they are related in some way through their alien or metahuman genetics. Another could be a villain who has the ability to manipulate time and space, causing chaos in both Smallville and Central City. This would force Clark and Barry to work together in ways they haven't before. A third plot twist might be that a character from Smallville who was thought to be normal actually has latent superpowers that are activated during the crossover, adding an unexpected element to the story.
Maybe in the fanfic, there's a villain who can absorb their powers. So when Supergirl and Flash first encounter this villain, they start losing their powers bit by bit. This forces them to rely on their wits and non - superhuman skills to outsmart the villain and find a way to regain their powers before it's too late.
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 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.
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.
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.
The Flash's ability to phase through objects could be combined with Agents of Shield's cloaking technology. Imagine if they could create a new device or power - up that allows an agent to not only be invisible but also phase through walls and security systems. And Cisco from The Flash could use his vibing ability to detect threats that Shield's sensors might miss. His knowledge of other dimensions could also help Shield better understand any interdimensional threats that they might face in a crossover scenario.
One exciting plot twist could be Ben using his alien forms in unexpected ways within the Attack on Titan world. For example, using Heatblast to melt through the Titans' hard exteriors in a crucial battle. Another could be a character from Attack on Titan getting the Omnitrix and having to learn how to use it. This would completely change the power dynamics in the story.
Maybe a character from Halo, like Master Chief, gets transported into the GI Joe universe. He has to adapt to their different warfare style and politics. Meanwhile, the GI Joe characters are in awe of his advanced armor and combat abilities. This creates a lot of interesting interactions as they try to figure out how to send him back while also using his skills to fight their own enemies.
One exciting plot twist could be Spider - Man's web - slinging abilities affecting the Grimm in RWBY. Maybe his webs are able to hold the Grimm in a way that the Huntsmen and Huntresses in RWBY have never seen before. This could change the way battles are fought. Another could be that Spider - Man has to adapt to the world of Remnant, where the rules of physics and combat are different from his own world. For example, he has to figure out how to deal with Dust, the energy source in RWBY, and incorporate it into his fighting style.