The Clandestine Corporation is an agency which was founded by Dan Mason from the remainments of the defunct secret society and criminal organisation the Clandestine Company. It consists of a team of black ops and field agents and primarily exists in order to deal with future threats to humanity, which is unlike their predecessor who wished to simply manipulate major catastrophes just to further their own goals.
Following the downfall of the Clandestine Company, remaining members made an attempt to salvage their technology and revive the group in order to try and continue their plans. They moved their operation to that of City 16 due to the destruction of City 17 and to once again work in secret. Dan Mason (a former agent) was seemingly brainwashed into serving the new Clandestine Company, which forced his friend Nathan Johnson (one of the main perpetrators in their downfall) to go on the run.
Despite this though, Dan used his position to get rid of the remaining links to the old Clandestine Company, and began to build it into a legitimate organisation and used their knowledge and findings to create a defense agency which would respond to any more impending attacks, primarily those of rogue aliens (just like the Combine or Race X species). Like Nathan, Dan foresaw that the Combine would one day return and built an elite to prepare for their arrival.