Without certified villains and bad guys, it's hard to have a proper setting. Someone has to be the assholes. Luckily, in the Cosmic Era, organized crime is big business, and as such there are several major terrorist groups, crime syndicates and megagangs.
Aka Cobra, the AC hearkens back to their antiquated biased misinformed idea of what 'Murica was and in the Cosmic Era, they fight to see that dream recovered. This generally involves primitive religious ideas, personal materialism, and rebellion against the pragmatism and collectivism of most of North America. Drawing from social outcastes, criminals, and disenfranchised veterans, the Command has turned most of the southern Rockies/North and central Texas into a North American version of Taliban Afghanistan. AC has indigenous support, access to heavy weaponry and military factories and can and does fight battles against the Atlantic Federation.
The biggest more organized criminal syndicate in the Eastern Hemisphere, this cartel of drug lords, gun smugglers, vice kings, political terrorists, despots and banana republic dictators have amassed a staggering amount of wealth from illegal shadowrunning, gambling, human and drug trafficking, and are among some of the worst people on the planet. Operating out of Indonesia and SE Asia, they are heavily armed, and have access to powerful arcanotech including major advancements in genetic modding and supersoldier information stolen from the PRC and the ACPS. Shadowlaw is well known for violence, staging martial arts tournaments, criminal biomodification, and torture.
Black Dragon Society
The Black Dragon is a massive guns, drugs, and money criminal organization that has a heavy hand and strong presence in the Western portion of North America and has made inroads in Central America, and the USSA. The Black Dragon is violent, remorseless, ruthless, and where they lack heavy weapons and advanced tech, they have numbers recruited from favela dwelling street gangs, disgraced mercenaries and discharged military and war criminals on their side.
A European threat, Armas wants to see Europe united again into an independent power, free of both the Federation and the Alliance. This has lead to constant violence and terrorism along the AtFed/EA border, and major hotspots in France, Italy, Spain, and the Balkan Peninsula (Shocking, I know). Armas is internationally savvy, as has allies with Amerikka Command and Shadowlaw facilitating the flow of technology, equipment, and information between these powers. While not a huge immediate threat, Armas and it's charming agents are the glue that hold the criminal underworld together.
A maritime terrorist/pirate organization, the Python Patrol operates out of Australia and Indonesia, where it is a threat to the PRC, the ACPS, and even clashes with the agents of Shadowlaw. The Patrol is heavily armed, psychotically violent, and receives funding from the government of Australia, as the Patrol has formed a strong buffer between the Land Down Under and China and it's regional ideas of Manifest Destiny. The Patrol is primarily a racist organization bent on hunting down ethnic Chinese and killing them.
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The Foot Clan, the Mafia, street gangs in the favelas and megaslums, Mad Gear Gang, Local Drug cartels, regional banditry and rogue mercenary organizations.