Command is a dumb artificial intelligence program that works for the Splinters. Its purpose is to communicate with the Red and Blue teams, give any kind of orders, ensure that they get needed supplies and maintain the facade of a normal functioning military. Command is located on a computer terminal in a cavern under the canyon.
Command rarely communicated with the 3rd Generation before medium and long-range communications were cut off by native aliens. Command believed that the canyon had been wiped out by the alien invasion, and a failsafe was activated to conceal the canyon and its experimental simulation for good. Without knowing that the failsafe itself had also failed, Command carried on and waited for further orders from the Splinters. Then when the aliens were defeated and comms were restored, Command slipped up and out of disbelief tipped off Meredith and Filch.
Meredith led an expedition into the caves after BASE tracked Command's signal. That was when they discovered the computer in the cavern and learned about the simulation. Command then wiped out all of its storage and self destructed, fearing that the Splinters would probably torture it.