The Shadow Agency is a shadowy organisation that was supposed to have disappeared years ago. It is also the place Killer Bean worked for.
Known members of the agency:
Leader of the Shadow Agency
The Shadow Agency was first mentioned by Detective Cromwell's partner. It was supposed to have shut down years before the events of this movie, but it hadn't. Supposedly, the Shadow Agency was a top secret branch of the government. The government would use this branch to do things they themselves couldn't do under the law, like murder people they have no solid evidence against. Eventually the government shut it down for fear they could be found out.
Now the Agency is running under its own rules and, like Vagan put it, is just a guns for hire.
Under Government Rule Edit
While the Agency was under the governments rule they followed suspicious persons to apprehend and/or kill them. The Shadow Beans (agents) would be sent out to observe people the government thought where no good. Vagan is known to have chased after one of those organisations for years.
After their shut down years before the events of the movie, the Shadow Agency became its own thing. The government have apparently turned their heads from them and so the Agency can do what they please. Now the Agency isn't at all like it was before, lending Agents to whoever can pay the most. Bad people and organisations which the Agency once persecuted are now being sold weapons and lent Agents for their own doing. Most Shadow Beans don't care about this, as the only known rouge is Dark Bean/Vagan.