Plot ideas
These are just some general ideas and I don't have ideas for every group yet. None of this stuff is in the works so feel free to make suggestions, extrapolations, or modifications of your own. None of these are set in stone as this thread is meant to get ideas out there.
Future Foundation: Still stinging from the failure of his last invasion years ago, Annihilus begins an experimental program to create super-powered insectoids to enhance his arm. He sens the first batch as a test against the Future Foundation.
X-Men: A rash of mutant disappearances causes the X-Men to investigate. This leads to discovering a resurgence of the organ-harvesting organization, the U-Men., which has become a fanatical pseudo-cult dedicated to the ascendance of the "Third Race".
Wild Pack: A mutant Somalian warlord that Daniel once thought dead is still alive and carving a path of destructive conquest in his country that could potentially destabilize the balance of power. The Pack is hired to take him out for good.
Outsiders: The team is contacted by members of the Mexican governments to save the son of a prominent government official being held hostage by a powerful new drug cartel. The team discovers that the cartel, which is growing in power and influence daily is in fact run by powerful metahumans, including a man who claims to be an avatar of Death.
Shadowpact: The team is sent to track down a group of demonic fugitives from Limbo that would not bow to Dante's rule. The group's goal is to release a powerful demon who once nearly usurped the rule of Satan (Marduk Kurios) centuries ago, who was too powerful for Satan to destroy outright so instead imprisoned on Earth.
Heroes for Hire: A variant of the Venom drug is being distributed on the streets. The users become murderous berserkers. Too much use leads to a failure of their internal organs to cope with the enhanced effects. In the course of defeating this epidemic, the Heroes discover rumors of a new Power Broker and the diary of Dr. Karl Malus.
Shield: The organization investigates what at first seems like a civil war within Hydra, only to discover that it's a mass infiltration of the terrorist group by the powerful cult, Kobra.