The Covert CIA Research Base was The Man in Black's facility used to research beings with paranormal powers in relation to military defense applications. The base was located off-site from the main CIA grounds.
After Erik was saved by Charles off the coast of Miami, the group went to the covert CIA research base to serve as their primary headquarters. Hank McCoy showed Charles the designs for the original X-Jet, based upon the military SR-71 Blackbird, and his prototype for the machine Cerebro located outside the facility. Through using Cerebro as a conduit for his telepathic abilities, Charles managed to track down several mutants for recruitment into Division X at the research base.
Whilst Charles, Erik, Moira MacTaggert and Levene were attempting to intercept Shaw's meeting with a Russian General, Sebastian Shaw sent his associate Emma Frost to meet with him on his behalf, instead deciding to pay Division X a visit to their base. Sebastian Shaw and his Hellfire Club henchmen Azazel and Riptide attacked the base, which resulted in the destruction of the original Cerebro, Angel Salvadore defecting to the Hellfire Club and the death of Darwin.
Following the attack and the exposure of the lengths Sebastian Shaw would go to, to ensure his plan's success, Charles relocated the remaining mutants into the Xavier Mansion in Westchester, New York, whereupon he resumed training the X-Men to harness and control their powers to their full extent in the fight against Shaw. What became of the Research Base is currently unknown.