Ye Olde Nuclear Silo

Every so often in Science Fiction that takes place in the Near Future or at least the not so distant future, there will be rebels, and all rebels need a suitable hideout. Maybe there's an abandoned warehouse or an empty cave, but that's only for rebels who don't have it in them to be a real rebel army.

If you're about to tell the evil government or the alien invaders who's about to be in charge here, you need a base that really brings the message around.

You need Ye Olde Nuclear Silo. Originally created in the Cold War or in preparation for World War III, nuclear silos provide everything a real rebel army needs: It's a miniature military base removed from larger settlements and hidden from most observers in the sky, has all the pipes and cables for the industrial feeling, and those gigantic, slow-moving doors! It usually comes conveniently with fully functioning computer equipment since it was already designed to survive armageddon, and it also provides that cozy damp cave atmosphere. If you're really lucky, it may even come with a functional missile and warhead.

Note that this trope extends to cover pretty much any other type of secret underground military installations.

Comic Books

 * The Morlocks from the X-Men live in tunnels under New York that were originally built as fallout shelters.

Film

 * In Stargate the military has hidden the titular gate in an old Cold War-era underground facility. Stargate SG-1, however, moved the gate to the US Air Force's Cheyenne Mountain facility, home of NORAD. (To this day there is a sign over a door at NORAD reading "Stargate Command." It leads to a broom closet.)
 * In Star Trek: First Contact, Zefram Cochrane's warp ship is kept in a nuclear silo. This is understandable, as the ship sits atop an intercontinental ballistic missile that's set to launch into space.
 * Day of the Dead had most of the zombie research take place in an old nuclear bunker. Oddly enough, the scientists who ran the place kept the first level of the bunker open and in disrepair, and allowed people to just wander in and out as they pleased, as a way of keeping the labs a secret.
 * The final scenes of Terminator 3 take place in one of these.

Literature

 * The Torturer's Guild headquarters in Gene Wolfe's The Shadow of the Torturer apparently consists of the disused shells of huge, ancient starships. The torturers sleep in cabins, with portholes, and a throwaway line mentions that the ship's original AI is still functioning, though extremely deranged.
 * Played very straight in the MechWarrior novel Ghost of Winter; the eventual ragged band of resistance fighters against the pirates who have taken over their planet (an ice world with only one major settlement) take shelter in an abandoned secret Clan depot that conveniently included a Star of 'Mechs. (Ironically, rumors of just that little 'treasure cache' were what drew the pirates to their world in the first place.)
 * Ardneh is revealed to be this at the end of Empire of the East.
 * Prince Roger: Thomas "Tomcat" Catrone got one of these as part of the bargain when he bought a plot of land in central Asia to retire and start a horse ranch on. Since his land already had this solid building with plenty of room, he's turned into a nice, well-appointed home.

Live Action TV

 * In Jeremiah, the titular character was based in an underground military facility, from which he ventured out into the post-apocalyptic world.
 * This was Cheyenne Mountain/NORAD again, although they rarely used the name. It seems a pretty popular choice.

Tabletop Games

 * In the Paranoia adventure The Yellow Clearance Black Box Blues, the Sierra Club secret society has a hidden base outside of Alpha Complex in an abandoned nuclear power plant.

Video Games

 * The Half Life series uses this trope a lot.
 * Black Mesa Research Facility in the first game is located inside the old facilities of an underground missile research center. Though actually a test room for rocket engines, the room with the tentacle aliens is practically a missile silo. Later there's an actual missile silo that holds a modified rocket that is used to launch a satellite into space, that was supposed to be used in a plan to seal the dimensional rift.
 * Actually, Black Mesa is basically divided in two parts: the new, spick-and-span office part, with the modern train system; and the old, unused (or barely used) old part, with the missile silo and the old rail system, with a lot of wooden barricades and boarded-up doors.
 * Half-Life 2 has the Black Mesa East rebel headquarter. Though apparently not an actual missile silo, it has all the other features of such a place.
 * The White Forest base from Episode 2, which serves as a replacement for Black Mesa East, fits the trope better: It is located in an actual nuclear missile silo, again hosting a rocket that is used to launch a satellite into space to seal a dimensional rift. This time it actually works.
 * The second level in Halo 3 takes place in an old missile silo that serves as the makeshift base for Terran forces in East Africa. At one point one of the soldiers actually remarks on its very Twenty First Century style, complete with ancient hydraulic doors.
 * The Fallout games live and breathe this trope.
 * Quite a few maps in Team Fortress 2 incorporate some kind of missile silo into the Bizarrchitecture.
 * A level in Deus Ex takes place entirely in and around a missile silo – nuke still included.
 * Target: Terror has a nuclear silo level.
 * In Star Control 2, the Earth ships rely on digging up leftover nuclear warheads from such silos.

Web Comics

 * While they can hardly be called rebels, the cast of User Friendly temporarily moved to an abandoned missile silo at one point. Hilarity ensued.

Western Animation

 * In Highlander the Animated Series, one of the first immortals the heroes meet holds the knowledge of nuclear weaponry. Conveniently, he lives in a missile silo.
 * In the Inspector Gadget episode "Down on the Farm", Dr. Claw attempts to launch a nuclear missile from a farm silo. This was during the Cold War, you know.
 * The Autobots of Transformers Prime are based in a nuclear silo. They have the permission of the government, and it's in the middle of nowhere,hidden underground, fortified and big enough to comfortably hold things on a Cybertronian scale, so it's an ideal base for them.

Real Life

 * You too can own one of these...
 * http://www.silohome.com/
 * http://www.missilebases.com/