The X-Files premise is that agencies such as the FBI and CIA encounter and investigate the paranormal, the extraterrestrial, and keep files on such encounters. This is quite true, but they are not termed X-Files. This data goes by many names, all designed to avoid drawing attention. The mazes within the intelligence agencies cause even their leadership to get lost. Such files were in existence before the alien presence became a hot topic, as what is termed paranormal, in the form of ghosts and poltergeist activity, has always been present. These files grew by a quantum leap, in pace with the Awakening, about the time of the Roswell incident.
With the X-Files series the secret government hit pay dirt. The series has been wildly popular, in no small part because the producer does not shy away from controversy - he embraces it. Thus, the series has been encouraged to be more and more bold, as MJ12 wishes the public to adapt to the reality of the alien presence and their government's role in this. Where at first the series flirted with abduction and human experimentation and only alluded to the cold hand of the CIA in suppressing information, the series was encouraged to get graphic and to make the CIA the villains they have, in truth, been. The secret government is multifaceted, and many parts did not participate in the brutality that the CIA presumed that secrecy called for. They wish to be disassociated, and where the true story will in all likelihood never be told, the X-Files is coming darn close to it.