Alternate Campaign: The Bureau for Paranormal Research and Defense
There was no sign on the building. No sign in the smallish parking lot. No sign on the glass door, nor any logo or similar design in the lobby or foyer of the building. The receptionist would happily guide visitors to meetings, but anyone without an appointment was escorted out the door by a squadron of security guards, most of whom had once been Secret Service or Marine Intelligence.
Take a bit of Raiders of the Lost Ark, The X-Files, Lovecraft's Chthulu mythos, mythological beasties, Chill's SAVE organization, and the Ghostbusters, and you might get something similar to Mike Mignola's Hellboy series. Published by Dark Horse Comics, Hellboy is about a paranormal investigator working for the Bureau for Paranormal Research and Defense (BPRD). Ghosts, demons, vampires, werewolves, zombies, and more are encountered by BPRD agents in their missions. Just the type of thing for the adventurous in the Sixth World.
Since the American government had been in charge of the operation that had resulted in Hellboy's discovery, they laid claim on him as if he were property. Despite Trevor Bruttenholm's furious protests -- he felt quite protective of their strange visitor -- the Americans brought Hellboy back from England with them.
The Bureau is based out of Fairfield, Connecticut, UCAS. The BPRD is similar to the United State's NSA (National Security Agency) in that it's a publicly known secret agency. Other organizations such as the FBI, CIA, and other intelligence and law enforcement organizations would know about it, but the average Joe might not.
The purview of the Bureau is to investigate magical threats and resolve them. While this poses some considerable overlap in jurisdiction for cases that deal with local police (who, in some cities, are actually corporations like Knight Errant or Lone Star), the Bureau doesn't waste resources on apprehending magicians wanted for burglary. Rather, the BPRD would send a field agent out on missions that range from stopping a serial killer mage to investigating magical artifacts to uncovering one of Winternight's plots.
Using the Bureau
The Bureau would, like the Double, Double Toil and Trouble campaign offered in the Shadowrun Companion, allow the characters to see the world. They might go to Poland on one mission, to the heart of the Siberian Wilderness another time, deep into the Yucatan next week, and into New York City after that. As a UCAS-run intelligence operation, they should have a power equal to the FBI in dealing with cases that rely heavily on the paranormal. As a privately funded organization, they could be the guys the FBI calls in when the Feds are in over their heads or want someone who's "experienced with this sort of thing".
Antagonists and Plot Ideas
Obstacles that the Bureau's agents may come up against could be the majors covered in Threats (The Atlantean Foundation, the Vampires, Winternight, Mr. Darke, the Gestalt), "typical" paranormal things (ghosts, werewolves, poltergeists), or anything that the Awakened world could throw at them. Find out what the secret of Innsmouth really is. How about a search for the Spear of Destiny or the Lost Ark? Have the adventurers investigate the murders of a magical cabal... The sky's the limit here. One of the particular nasty things you might want to try is have the characters investigate the Polish Incident from Mayfair's Chill RPG (it's in the Werewolves supplement). Or use any of that game system's adventures in your BPRD campaign.
Although a mundane character can be played in this type of campaign, they would be rare for a PC. Almost all the characters would have some sort of magical ability, either some sort of adept or magician, although not every encounter will be one that is defeated by magic. The Bureau would have its own initiate order and the player characters would be invited to enter as soon as they are able to. When you go against the baddest mojo in Shadowrun, it would be nice to be ready for them.
Speaking of being ready, the players will not have to worry too much about gear as the Bureau would provide all equipment the Bureau decides the characters need. That means that you, the GM, can outfit the player characters with whatever you want them to have. Like the Special Forces campaign type, these characters already get paid a set amount each year, enough for a Middle Lifestyle. Also, like the Special Forces PCs, one of their free contacts is already chosen -- the Bureau.