Central Metro Command

Central Metro Command was an organization hastily assembled in the immediate aftermath of World War III in an attempt to create some order amongst the survivors who had fled into the Metro.

Overview
When the air raid sirens were sounded in Moscow, around July 2013, thousands of Russians fled for safety into the Metro - depending on the source, there were anything from 40,000 to 250,000 who originally sought shelter (though the numbers are now far fewer as a result of wars and mutant attacks) inside the Metro. Among them were soldiers of the Russian Federation, high ranking officials and policemen, and politicians, all of whom had direct links to the Metro from their government buildings. These men and women, being seen as figures of power, took control of the refugees and tried to organize them.

Many Metro dwellers originally believed that the President and his cabinet had fled from the fallout into secret bunkers behind the Ural Mountains, and that they would soon return to assume control and rebuild their shattered country - this rumor could possibly have been propagated by Metro Command to keep up morale, or they may have actually had contact with the President for a while, though eventually, all outside contact was lost.

It is unclear how effective Central Metro Command was in organizing the Metro dwellers, but within a few years, likely as it became clear there was no rescue coming and that the surface was irradiated and they could not return to it, the command structure began to break down - the unified Metro collapsed into small city stations. Isolated stations grew wary of each other and fighting began to break out. Central Command had completely collapsed, its remnants lasted as long as possible in D6, and any semblance of pre-war Russia was gone. The survivors of humanity's final war were forced to remain underground, seeking an existence from scraps and the remains of the old world, where they remain to this day, awaiting the time when they can finally return to the surface and rebuild.

Metro: Last Light
Though Metro Command has long since dispersed by the events of Metro: Last Light, Metro Command is referenced numerous times and may be the player faction in the Tower Pack DLC. If this is the case, then Metro Command is shown to have less of a role as what might have been thought previously. Metro Command is shown to take a passive role in the happenings of the metro, more as guilt-ridden observers than participants. Still in possession of powerful technology, Chukotski and the Captain in the Tower Pack may be part of this group of soldiers and scientists hiding inside D6 after the war, who have continued to work as long as they can. It's unknown what happened to Metro Command, and what led to their downfall. It is stated by Su and Bar that after the bombs fell, pre-war scientists inside D6 sealed themselves in the facility, possibly to contain the viruses inside, though the power fluctuations in the simulator might reflect something significantly wrong with the reactor.

Trivia

 * It's unknown whether the Rangers found any bodies inside D6 when they captured it - it is possible all the remaining scientists were devoured by the biomass.
 * Many other governmental buildings, like the Kremlin, did not connect directly to the Metro, but rather to the secret Metro 2 tunnels. These survivors may have tried to create order themselves and were likely better equipped to deal with it. However, by 2033, most had either been killed or joined the regular Metro, as no survivors live in Metro 2 (aside from D6).
 * It's possible that the Central Metro Command became or had always been what are known as the Invisible Watchers, taking extremely secret and indirect control of the entire Metro after supposedly collapsing.