Elaborate Underground Base

"JGSDF Soldier: Who are you?

Sam Fisher: I'm the guy who's here to save the world.

JGSDF Soldier: I thought I was the good guy....

Sam Fisher: No, no. You're on the team with the super-secret underground base. I'm the guy breaking into the base. That makes me the good guy."

- Splinter Cell: Chaos Theory

To maintain Plausible Deniability and hide from magical TV Spy Satellites, any sufficiently powerful or advanced covert organization of heroes, villains, conspirators, or military personnel needs an Elaborate Underground Base to use as their headquarters and hide their Applied Phlebotinum. After the End, or in preparation for The End of the World As We Know It, openly known organizations may elect to move Beneath the Earth as well. And it's a good location for a Supervillain Lair.

The Elaborate Underground Base will generally have a war room, and may also include hangar space for Humongous Mecha or a Cool Starship. Particularly large examples may be the size of an entire city, and might include hydroponics bays for growing food or even actual fields of crops lit by sun lamps. The larger sizes of Elaborate Underground Base frequently serve as an Adventure Town; the smaller ones are frequently the setting for a Bottle Episode.

Particularly secretive organizations may hide their Elaborate Underground Base in the middle of a city, and include lots of elevators, trams, pneumatic tubes, and other means of transportation between the base and hidden chambers in buildings on the surface.

Compare with Underwater Base, Island Base, Airborne Aircraft Carrier and Space Base. See Beneath the Earth for a related phenomenon, minus the Applied Phlebotinum. May induce Sigil Spam if the organization really loves their logo.

Anime and Manga

 * Neon Genesis Evangelion has NERV setting up shop inside the GeoFront, a massive cavern that is actually just the upper 11% of an even larger spherical cave almost completely filled up with earth and rock debris. And going Up to Eleven, Terminal Dogma is an Elaborate Underground Base built below another Elaborate Underground Base.
 * Not really. Terminal Dogma is a more-or-less natural cavern system. Well, as natural as caves inside a spherical asteroid carrying an alien terraforming device can get.
 * The Island of Bardos from Mazinger Z: Dr. Hell set his first base in the subterranean mazes of that island, building all what he needed for his Supervillain Lair: a war room for planning strategies, private chambers for his Co Dragons, barracks for his Mooks, several hangars, laboratories to build weapons, Humongous Mecha and cyborgs, training fields for his troops and Robeasts, his throne room...
 * Dr. Kabuto's lab basement also counts. It was hilariously lampshaded by Kouji in the original manga (since Juzo had built Mazinger Z in his home in the middle of a city whereas his anime version did it in his mansion located in Mount Fuji), when he found the entrance and asked: "Since when is there a basement in the garden?"
 * Great Mazinger: Mykene were a civilization had lived underground for millennia, so their entire empire -an intrincate network of caves and caverns- was an Elaborate Underground Base.
 * Jaburo of Mobile Suit Gundam. Granted that it's only seen in a few episodes of the original series before being blown away in Mobile Suit Zeta Gundam, but it does get additional screentime in Stardust Memory and MS IGLOO.
 * Numerous Galactor bases on Science Ninja Team Gatchaman fall under this heading. By extension, enemy bases on the Americanized versions.
 * Father has the entire area underneath Central!
 * The manga and live action of Sailor Moon have an underground base under the Local Hangout.
 * Macross/Robotech have an underground base in Alaska (possibly in the site of the real life Elmendorf AFB), armed with the BFG of the Wave Motion Guns. Incidentally, Macross' secondary sources list four other identical bases being build when the Zentradi launch the final attack, one of them in the same area of Jaburo.
 * The Autobots' base in Transformers Cybertron. Mineral deposits prevent sensor scans of any kind from detecting that the terrain has been hollowed, but the equipment had to be painted with a stealth coating to prevent the Decepticons from detecting it.
 * One of Doraemon`s future gadgets allow instant creation of Elaborate Underground Base. It can be big enough to become a city of its own, which Nobita then exploit to create his own dictatorship (Played for Laughs). However, one of the movie deal with the sinister encounter with The Reptilians when Nobita and co Dug Too Deep...
 * The main characters' HQ in Senki Zesshou Symphogear.

Comic Books
"Unless...this whole thing, it's...it's...NON-UNION! The horror...the horror..."
 * The Batcave from the various Batman series.
 * The original headquarters of the Justice League was an elaborate base built into the base of a mountain. Several other teams have taken this base out of mothballs, such as Young Justice.
 * PS 238, the school for children of superheroes, is in an Elaborate Underground Base beneath an actual elementary school.
 * Xavier's mansion of the X-Men is usually presented as being only living quarters and classrooms for students and staff; the actual base of operations is underground.
 * The Thunderbolts have their base located inside a mountain.
 * G.I. Joe is rife with these. The original Joe base, "The Pit", is hidden underneath the chaplain's assistants' motor pool at Ft. Wadsworth in Staten Island. When this is destroyed by Cobra, a new Pit is built out in the desert. And Cobra has a fair number of secret bases themselves, including an entire town brimming with underground evil.
 * During the Silver Age, Lex Luthor's "Luthor's Lairs" numbered in the hundreds, and could be found anywhere. At least one of them lasted until the 30th Century, showing up in a Legion of Super-Heroes story where the outlawed Legionnaires make use of it to not only get new outfits again, but find out what caused the populace to turn against them.
 * During the Hydra arc of JMS's run on Spider-Man, Peter wonders how HYRDA can build one of these in New York while it's taken the city three extra months to finish a subway extension.

"Cyclops: Our antagonist has serious infrastructure. I have a feeling we're going to see a classic James-Bond-Villain Crazy-Man base make itself known in a few moments.
 * Warren Ellis' Hangs a Lampshade on the subject in Astonishing X Men #34 - then deconstructs it as grotesque with the very next sentence.

Beast: I'm always up for a Doctor Crazy-Pants volcano headquarters.

Cyclops: This is the bit that really annoys me. All the things in this world that can be fixed with money? And every time it's "Well, I've got all this cash, but I bought myself an asteroid hideout instead."

Beast: Aaah. That, my friend, is indeed classic."


 * In the Zorro comics written by Don McGregor (for Topps and Dynamite), Zorro has an elaborate underground base that rivals the Batcave.

Film
"Mike: "Wow, occasionally a spelunker just wanders in! "Hey, what the hell?!""
 * THX 1138
 * Logan's Run
 * In X2: X-Men United the underground base becomes a plot element when the Spy Satellites actually detect the Cool Ship in its hangar underneath the Mutant Academy. William Stryker uses this evidence to convince the President to okay a commando strike on the school, secretly to further his plan to wipe out all mutantkind. Stryker's also got an Elaborate Underground Base of his own.
 * Zion in The Matrix. A Very Elaborate Underground Base and a full blown city.
 * Dr. Evil from Austin Powers has an underground lair.
 * Sky Captain and The World of Tomorrow (2004). Mad Scientist Dr Totenkopf has a base populated by hordes of flying killer robots that is large enough to contain a brobdingnagian Raygun Gothic rocketship.
 * The Avengers 1998. Sir August's underground base, which is on an island in the Thames in London.
 * James Bond, amazingly enough, has very few of these, despite the series being ridden with cartoon villans and conspirators. The closest they ever got were the hollowed-out volcano complex in You Only Live Twice and Drax's Amazon launch facility in Moonraker.
 * Goldeneye had an elaborate underground military bunker at Severnaya, and the Big Bad's Lair is actually below the giant pool where the cradle antenna is hidden.
 * Dr. No had an elaborate nuclear facility but it's not clear that it was underground. Although fairly likely, given that it explicitly is in the book and in the film they dine in a glass-windowed room below the waterline and thus presumably underground as well.
 * In Hellboy, Rasputin has an underground lair
 * Hollow Man - Secret underground lab
 * The supercriminal Diabolik in the movie Danger Diabolik has a huge underground lair. The movie was shown as the last Mystery Science Theater 3000 episode:


 * The Island: An underground base is used to.
 * Team America, in Team America World Police, had an elaborate base inside Mount Rushmore.
 * The HYDRA facilities in Captain America the First Avenger are above ground and in the open, and their main base is dug into the Alps, and is implied to be 500 feet underground. In addition, the SSR's main base is hidden within various old stores in Brooklyn.

Literature

 * The Illuminati's Bavarian headquarters in Duumvirate is one of these. Parts of it are a couple of centuries old.
 * David Wingrove's Chung Kuo has a series of underground bases in the Alps, the only part of Europe that is not occupied by the City or its plantations
 * The Wildfire facility in The Andromeda Strain. The only entrance is the elevator shed, and the facility topside is what it's disguised as - a wheat modifying facility.
 * Willy Wonka's crazy factory in Charlie and The Chocolate Factory is mostly underground. The book contains an explicit explanation of this by Wonka, where he tells everyone that he decided to expand his factory by tunnelling downward and outward so that he could basically expand indefinitely without ever having to buy any more land or pay any rent to the property owners most of his factory is under. This would, of course, be all kinds of illegal in real life, but Wonka doesn't care.
 * A similar rationale obtains for the enormous set of underground tunnels built by the deep-down dwarfs in Ankh-Morpork in Terry Pratchett's Discworld novels. By digging under the city, they can create their own dwarfs-only authentic dwarf mine under the city, unbeholden to city law or city rents. After the events of the book Thud!, the deep-downers are thoroughly discredited and Lord Vetinari appropriates their delve for the city government. (It is heavily implied that these tunnels will form the basis of a future Ankh-Morpork subway system.)

And the dwarfs have better legal standing than Wonka, considering that on parts of the Disc that dwarfs normally live, such as the Ramtops and Überwald, dwarf-law does cover the underground and is entirely separate from surface law. This just isn't true on the Sto Plains.

The bulk of Dwarf civilization away from Ank-Morpork is also mostly underground. There are huge cities.
 * Supervillain Doctor Impossible of Soon I Will Be Invincible has a base descending deep into the Earth: when he returns to it after his last defeat, the deeper levels are still intact. Also, his first base was dug down from the basement of an ordinary suburban house.
 * Super Hero School Whateley Academy in the Whateley Universe has extensive underground stuff. Powers testing, deviser workshops, arenas, you name it. And that doesn't even cover the highly dangerous sewer system there. Lampshaded by mentions that they now have to be quite careful where and how much they dig, in order to avoid having the above-ground structures fall into a sinkhole.
 * Center, The Chessmaster AI of The General series located in a warren of abandoned hi-tech tunnels deep beneath East residence. It is unclear whether this ancient HQ was designed to be underground or has been buried by subsistence over the millennia since the Fall.
 * Salamandastron for the Long Patrol, and the Kingdom of Malkariss for one set of baddies, in the Redwall books.
 * Tolkien was big on these, both for good and bad guys. In The Hobbit, you have dwarf fortress in the Lonely Mountain (owned by Smaug the dragon). In The Lord of the Rings you have Moria, also mostly dwarven but built with some assistance from the high elves. Melkor, the Big Bad of The Silmarillion had Utumno, which amounted to an underground country and Angband (whose excavation produced enough refuse and slag to pile into three 10km high mountains), and (somewhat unusually) elven underground fortresses in the form of Nargothrond (built with some assistance from the dwarves, pwned by Glaurung the dragon) and Menegroth (also built with dwarven help).

The Hobbit mentioned a few elven cultures, one of which was the "deep elves," which might refer to the Noldor who lived in places like Nargothrond (though canonically, the underground-dwelling Wood Elves of Mirkwood are separate from the Noldor). Underground elves are rather unusual... perhaps the assumption that Our Elves Are Better means they don't live in holes in the ground anymore. Only dark elves would do that sort of thing nowadays.

While, contrary to tradition, Elves of all kinds (Noldor and Sindar- see Menegroth or Thranduil's halls) do live underground in Tolkien's books, it's fair to assume that "deep-elves" in that case, as in the Lost tales, refers to "Gnomes", or Noldor, Elves which are deep in knowledge and thought, not Elves who dwell underground.

The Dead Men of Dunharrow lived in an elaborate system of caves in the mountains. Even 3,000 years after they died.
 * The Alchemists' Guild in A Song of Ice and Fire has an elaborate underground Guildhall composed of a labyrinth of tunnels, cells, halls, and warehouses filled with highly explosive wildfire. The place is designed to limit the damage should a cache of wildfire combust.
 * Stephenie Meyer's The Host
 * In the Dale Brown novel Fatal Terrain, Taiwan has a secret underground air base.
 * In Kim Newman's short story Swellhead, the the ghostly remains of the Elaborate Underground Base of a supervillain from an Alternate Universe is beginning to seep into our world with disastrous consequences.
 * The Yeerk Pool in Animorphs
 * The government's Daemon task force base is largely underground. The trope is subverted (in a moment that is simultaneously hilarious and horrifying) in that the Daemon's operatives
 * The sapient rats from Mrs Frisby And The Rats Of NIMH built themselves a Mouse World version of this trope under the farm. No actual Applied Phlebotinum is present by human standards, but by the standards of other animals it's a regular Mad Scientist Laboratory.
 * The Ministry of Magic in Harry Potter is completely underground that can be reached via elevator telephone booth, flushing down magic toilets (no joke), Apparation or Floo powder.
 * Dénis Lindbohm's Frostens barn (Children of the Frost, given the context of the story) features this trope as the home of the surviving remnants of humanity and their descendants, with them living in an increasingly sprawling set of constructions under the Scandinavian Mountains. In story, more installations were supposed to be built... but they were either unfinished or sabotaged when World War III came.
 * In Star Trek the Genesis Wave, the Lomarians (Plant Aliens responsible for unleashing the titular weapon) have one of these. It's justified in that the ecological devastation on Lomar has forced their people underground.
 * In the Time Scout series, half the action takes place on time terminal 86, in a winding cavernous complex in the heart of a Tibetan mountain in 1912.
 * The Hunger Games gives us, which is extraordinarily large.
 * The Observatory in Septimus Heap is heavily hinted at to be this.

Live Action TV
"Buffy: You said it was big. You didn't say it was huge.
 * Gerry Anderson seems quite fond of this one.
 * In Joe 90 the BIG RAT was located in a secret underground facility beneath Professor McClaine's house.
 * In Stingray, during alerts the entire city of Marineville can descend into a secure underground facility on hydraulic jacks. (Just in case anyone thought Neon Genesis Evangelion did that first...)
 * Thunderbirds of course had the Thunderbird hangars beneath Tracy Island.
 * SHADO Headquarters in UFO is located beneath a film studio. Think about it...
 * The second season of Space 1999 saw the command team move from the above-ground "Main Mission" set to a "Command Center" located deep underground.
 * Season four of Buffy the Vampire Slayer featured a military organization called The Initiative with a massive high-tech base underneath Sunnydale, where they held demons captive and used them for medical experiments. The Master's lair in season one also fits the trope.

Riley: I don't like to brag."

"Rupesh: "What's in there?"
 * In the Doctor Who episode "The Runaway Bride", The Doctor finds an elaborate ex-Torchwood One research facilty beneath the Thames river in London.
 * Of course, that's far from the only Doctor Who example. In particular, the Silurians are fond of these.
 * Also seen in The Sun Makers, filmed in the real-life deep air raid shelters of London.
 * Sheriff Jack Carter in Eureka lives in an experimental intelligent house that is underground. It doesn't fulfill all of the requirements, but it's underground, it's where he lives, and it's full of exciting gadgets, so it counts.
 * In Hogan's Heroes, the Allied POWs/spies had a network of tunnels under Stalag 13, to which Colonel Klink was consistently oblivious -- not the sort of cramped tunnels POWs might dig with spoons, but what you would find in a long-worked industrial mine. How the tunnels had been dug undetected was never explained.
 * Lampshaded in one episode in which the grounds have even more snow than usual, and the POWs have built a snowman. At one point, Col. Hogan indicates a particular patch of dirt and claims that it is "the only spot in camp that doesn't have a tunnel under it."
 * Most of the Dharma stations on Lost are partially or completely underground, and are of varying complexity. The Pearl and the Orchid are entirely underground. The Orchid is quite elaborate
 * Deep 13, from Mystery Science Theater 3000, supposedly. As noted, there is also one in the series finale, in the movie Danger Diabolik.
 * Neil Gaiman's Neverwhere features an entire sub-culture beneath London. There were also undergrounds beneath every major city on Earth, each distinctively dangerous. At least according to Huntress.
 * Power Rangers uses this quite often. Some seasons, such as the original, simply imply it, while others are more blatant about it. The fifteenth season, Operation Overdrive, commonly does a cutaway to the base by showing the aboveground mansion, and then dropping the camera via CGI through several layers of planetary crust. For added hijinks, the Rangers in this season are implied to be sliding down kilometer-length fireman poles to reach said base. And on top of that, they have three Humongous Mecha and a Cool Ship hidden inside.
 * British puppet character Roland Rat was originally supposed to live in the sewers beneath King's Cross railway station. In Roland Rat: The Series this suddenly became "the Ratcave"; an Elaborate Underground Base containing living quarters, a talk show studio and a reception area, and accessed from a hidden lift in a workman's shelter outside the station.
 * Ryukendo has such a base hidden beneath a police station, accessed by praying to the elevator (really). It also serves as a Haunted Headquarters.
 * In Stargate SG-1, Stargate Command functions as an Elaborate Underground Base that includes a functioning interplanetary wormhole (see "Real Life" example, below). In later seasons, the "Alpha Site", "Beta Site" and "Gamma Site" are all built as copies of the SGC on other planets.
 * The Genii of Stargate Atlantis act like Space Amish while actually living in these. Their true nature gradually becomes one of the worst-kept secrets in galaxy.
 * The 60's series The Time Tunnel featured a colossal underground base that housed the titular Time Travel device.
 * Torchwood Three in Torchwood is hidden under Roald Dahl Plass, Cardiff. This is in stark contrast to Torchwood One's tower in Doctor Who, which is Canary Wharf. The Torchwood Three base was a deviation from the classic luxurious underground base -- aside from the central hub, it was a rat-nest of cramped rooms and converted tunnels that have been repurposed and rebuilt over decades, it was dim and dingy, and water was always leaking in from Tiger Bay. The trope is Lampshaded in Children of Earth.

Gwen: "Big...science fiction superbase. Honestly!""


 * M.I. 9 has an Elaborate Underground Base concelaed beneath St Hope's School in MI High. Given it houses only three operatives and their handler, it does seem somewhat like overkill.
 * The Avengers episode "The Living Dead" had a huge underground city built by the villains for the purpose of raising an army.
 * The Dollhouse underneath Los Angeles is pretty much a self-sustaining spa eight stories down.
 * Xenon Base in Blakes Seven was an Elaborate Underground Base owned by a Villain of the Week. Upon his death, the heroes moved in and made it their base of operations for the remainder of the season. When you are a marginal band of outlaws facing a star-spanning empire, there is significant psychological comfort of being hidden under megatons of rock.
 * Season 4 of Alias introduced APO, a black-ops branch of the CIA (that most of the CIA doesn't know about) located underneath Los Angeles and accessed by the subway.
 * Alias was always radically unrealistic...in an oddly gritty way. The first three seasons took a great deal of care that the actions and settings of the heroes and villains made sense on their own terms. That is, given the weird premises of the setting, the actions and places made a great deal of logical sense. In Seasons Four and Five they threw all that aside and started making it all up as they went along, and it showed, as in nonsense like APO HQ.
 * Case in point, in one scene in season 3, they're bringing a Master Villain (Arvin Sloane) into the Rotunda, the top secret HQ of a joint CIA/FBI/Other task force, and they made a visible point of locking all the computers, securing everything remotely 'sensitive', and the villain is brought in blindfolded and ear-plugged to keep the location and details secret from him. In season five, they bring the master villainess Irina Derevko, almost as dangerous as Sloane, into APO HQ with no precautions at all. The writers just stopped trying or caring.

Tabletop Games

 * Alpha Complex from Paranoia is usually an elaborate underground warren with all the super-science facilities you could ever need.
 * The dwarves of Warhammer live in huge undergound cities, following the example set by JRR Tolkien. And the Skaven live below those in big cities and tunnels that span every continent.
 * Warhammer 40000 gives us the planet of Calth in the Ultramar sector, where this is the only kind of base because the sun is deadly. Necron tomb complexes also qualify.
 * Despite the name, virtually none of the "dungeons" in any Dungeons & Dragons campaign are prisons. They're either natural caverns full of unintelligent monsters (rare), tombs full of undead (uncommon), or this trope for the Villain of the Week (extremely common).

Taking this to its logical extreme is Malsheem, fortress of Asmodeus, god of sin and tyranny and lord of devils. As the fourth edition has transformed the Nine Hells into a planet, Asmodeus' fortress is comprised of the entire core of that planet.
 * The entire raison d'etre of House Telamones, Nosferatu bloodline from Vampire: The Requiem. They build elaborate underground bases to suit the tastes of their undead betters, but woe to the Would-Be Vampire Overlord who accepts the bid from a competing firm... it's mentioned in the text that House Telamones has BLOWN UP an entire CITY BLOCK OF SEATTLE rather than lose a bid.

Theater

 * The prototypical Elaborate Underground Base may well be Erik's lair under the Paris Opera in the various incarnations of The Phantom of the Opera, making this Older Than Radio.

Video Games

 * The whole of Breath of Fire V takes place in a geofront like super cave.


 * A few games have appeared where constructing an Elaborate Underground Base is a major aspect of the gameplay, notably:
 * The Dungeon Keeper series
 * Evil Genius
 * Dwarf Fortress
 * Although you don't technically have to do that (one of the DF Wiki's "optional goals" is to create a fortress that is based entirely around surface structures).
 * Minecraft
 * Bio Shock takes place in a underwater city/base named Rapture, where Applied Phlebotinum is developed, refined, and horribly goes wrong - the player's stated goal is to get out alive.


 * City of Heroes features this to an almost ridiculous extent. The Cobra-wannabe Council (formerly the Fifth Column) generally base themselves in converted caves, as do the Rikti, and even the evil cultist Circle of Thorns have their ancient underground city. The Faultline zone (former Scrappy Level Rescued From the Scrappy Heap) is said to be filled with former superhero bases that were abandoned in the earthquake that gave the zone its name, and people are trying to dig them up...
 * Not to mention the Shadow Shard - an alternate dimension seemingly comprised entirely of floating islands in the sky, with caves and bases dug into them anyway. If the game world had a consistent geometry, it'd likely resemble a very big ant hill with more empty space than rock.
 * Pokémon Red and Blue and Gold and Silver and their remakes have the Team Rocket bases, which is actually pretty elaborate considering they tend to build them under game corners and converted ninja bases.
 * The Spin Off games Pokémon Colosseum and XD had the Cipher base, which was rather complex. The only thing is, there was one floor on the upper level that was actually important for getting through the base (the button needed to unlock the door was there), so it can't be considered a true base.
 * As well as the first Pokémon Ranger, where the Go-Rock Squad's base is underground in a mountain.
 * The No One Lives Forever series had a couple. The first game had one in the US Pacific Northwest and an underground rocket launch facility somewhere in the South Pacific. The 2nd had an underwater base you had to infiltrate.
 * In the Command and Conquer series, nearly all of the Brotherhood of Nod's military facilities have some kind of extensive underground component. For example, the Hand of Nod has a massive training and fitness area, as well as a mock-up forest environment for combat practice, and an interrogation cellar.
 * Expanding on that, in Red Alert, there were the beautiful and famed internal missions. With computer consoles that actually did things.
 * From the Fallout RPGs, the various Vaults.
 * Fallout had the Glow, the Mariposa Military Base and the Brotherhood's Lost Hills HQ.
 * Fallout 2 had the Sierra Army Depot and the Hubologist base. The Brotherhood bunkers in the Den, NCR and San Francisco might also count.
 * Fallout 3 had Raven Rock and the Rockland comm. facility.
 * Fallout Tactics had the Brotherhood bunkers and Vault 0 which was simply the Cheyenne Mountain Complex coverted into an even larger facility.
 * F.E.A.R.'s Armacham Technology Corporation established the main facility for the Origin Project in an old military-industrial complex, and built the entire facility deep underground. Emphasis placed on the past tense, what with the explosive ending of the first game.
 * Project Origin takes it even further. The Auburn Memorial Hospital is a full-sized building constructed underground inside another Elaborate Underground Base. Wade Elementary has another Elaborate Underground Base beneath it. And that's before you get to the giant tram tunnels running through titanic chambers that include a Replica storage facility and massive maintenance area. Pretty much the entirety of Fairport is riddled with Armacham secret bases.
 * One wonders how nobody found out about it or that all the excavations didn't fatally weaken the ground.
 * Final Fantasy V had the Catapult, an underground/underwater base of Lost Technology. Among other things, it features an airship docking bay, a teleporter and a ship-sized elevator to the sea surface. And the icing on the cake? It's yours now.
 * Black Mesa Research Facility in Half Life.
 * The Aperture Science Enrichment Center in Portal is located, per the supplementary material, in an abandoned salt mine in Cleveland, Ohio. Portal 2 bizarrely retcons this to be in Michigan, but also takes the player on an exploration of the true vastness of the place. Elaborate barely even begins to describe it: some parts of the game take place as much as five kilometers underground, and the player is treated to vistas of immense facilities stretching as far as the eye can see, constructed over a period of at least fifty years.
 * The entirity of Overblood takes place in one.
 * Gears of War features the hollow, which is home to the entire Locust civilization. It runs all throughout the planet and there are areas inside of it big enough to have skyscrapers and air patrols.
 * Halo
 * Every single Forerunner Halo installation in the Halo universe is built underground. Presumably, this is so that experiments could be performed on the surface, while the Forerunners would stay underground to monitor the results.
 * Halo 3 - the second level takes place in Crow's Nest, an "old 20th century" military base inside Mount Kilimanjaro, which has been re-activated after the Covenant took over Earth. This base comes fully equipped with a hangar bay, hidden landing pads, big imposing steel doors and a war room, complete with big screens and Bridge Bunnies.
 * Metro 2033 features the entire subway system of Moscow, which is home to the remnants of civilization. It also features huge military installations even below that.
 * In Resident Evil, seemingly every building in Raccoon City, or in the forests surrounding it, has at least one well hidden elevator leading into one of the multiple underground Umbrella Corporation labs (which makes sense when you consider that Umbrella essentially owns and runs the city).
 * The British army in Resistance: Fall of Man has two underground bases from which they were staging their attacks on the Chimera. Extra content reveals that they had a third underground base, but it was flooded by the Chimera before the start of the game.
 * Skies of Arcadia has elaborate underground bases for both the heroes and the villains.
 * In World of Warcraft, the Dark Iron Dwarves have their own underground base in Blackrock Mountain. Technically so does the Dark Horde and Nefarian, since their towering base is built inside a volcano's cone.
 * The Defias Brotherhood has the extensive Deadmines, a combination mining facility, smelter, sawmill, and wetdock.
 * The Scholomance is a large school dedicated to dark magic carved out of the crypts of a castle. The Undercity is much the same, only it was built under an entire city.
 * The entire kingdom of the Nerubians was built underground, as is much of the temple to C'thun.
 * In Thief II: The Metal Age, the Cetus Project is run from Markham's Isle, a former pirate base taken over by the Mechanists. As you learn when you go there, the administration of the project is a bit complicated, but Markham's Isle certainly fits the Island Base and Elaborate Underground Base tropes.
 * The X-COM franchise. All of the X-Com bases (situated and built, room by room, by the player) were only accessible through the main elevator and the vehicle hangars, which affected gameplay if the aliens located said bases and attacked them with a relatively manageable number of alien foot-soldiers.
 * Same goes for Alien Bases, including the . Crosses over with Underwater Base in the case of the Colonies and Artifact Sites from Terror From the Deep, which are underground installations built on the ocean floor.
 * Deus Ex concludes in 's base beneath Area 51. On the good side, Tracer Tong has a sophisticated laboratory several floors beneath his Triad's compound.
 * The Elder Scrolls III Morrowind had a pretty large numbers of natural caves, often inhabited by smugglers. Most were small, like 2 or 3 rooms furnished with hammocks, candles and crates, but some other were kind of large, hosting a whole guild and richly decorated and furnished.
 * In Oblivion you can get one for yourself via the Thieves Den DLC. It is pirate-themed and has once taken over you can recruit pirates to give services(like skill-training and selling stuff like lockpicks) and go out stealing for your benefit.
 * The area under the Optimology building in 6 days a Sacrifice counts.
 * In Gaberial Knight:Sins of the Fathers, the Voodoo Cartel has one . God knows how they managed to put that in without anyone noticing.
 * In the first Mega Man Zero game, the La Résistance's base is located underneath an abandoned city. While the "base" itself is run-down, there are still some machinery functioning there, like an elevator and a teleporter. The base, after numerous attacks, was completely abandoned by the group in favor of a more elaborate, newer base (although it's not underground anymore).
 * Most Space Pirate bases in Metroid games tend to be these. Probably because both their homeworld and their main base at Zebes are plagued by near-constant acid rain.
 * Shadow Complex is a Metroidvania game that takes place in one gigantic base.
 * Naoto's dungeon in Persona 4 is one of these.
 * The Alpha Protocol base in, well, Alpha Protocol is a large underground complex apparently located somewhere in the American northwest. Reaching it is pretty difficult; agents are sedated into unconsciousness and transported to the location, via aircraft and boat in order to keep the base's location secret.
 * Colossal Cave, including the maze of twisty little passages, all alike.
 * The Zork games take this to an extreme, what with most of the games taking place mostly in the Great Underground Empire.
 * Fort Schmerzen in Medal of Honor and Allied Assault.
 * The Descent series lives for this trope. Granted, a lot of them are mines, but there are a bunch of military, scientific, and testing facilities as well. Of particular note is the final level of Descent 3, Dravis' Stronghold.
 * In Metal Gear 1 and Metal Gear Solid, the titular Humongous Mecha is hidden in one of these.
 * Metal Gear 2 has a variation: Although Metal Gear D is fought in the third (sixth?) basement floor of the main building of Zanzibar Land's detention center, it is not specified if it was actually the main hangar for Metal Gear D. Similarly, the Big Shell is technically above ground (or in this case, above water), but it is disguised so well as a cleanup facility that the personnel could literally get away with having armed forces stationed there as well as developing Arsenal Gear without the populace ever suspecting anything.
 * This seems to be fusing metal gear two, and metal gear solid two.
 * In Metal Gear Solid Portable Ops, there are three elaborate underground bases: One is the Nuclear Storage Facility (which is the deepest mapped area of the game), another is the Silo Complex (which is pretty deep underground, although the mapped areas themselves are actually shallower than the Nuclear Storage Facility), and it was originally intended in-game to have more than one missile silo. The last one isn't actually visited by the Player:
 * In Metal Gear Solid Peace Walker, both the heroes and the villains have elaborate bases: The Peace Sentinels had an AI Weapon assembly plant situated within a pumped storage hydroelectric power plant within Irazu's crater, an AI programming lab constructed either within an unknown ruin or an AI lab disguised as a ruin (Paz's description of the plant makes the ruin's exact origin a bit ambiguous), and an AI Weapons forwarding/Peace Walker construction base built within a gold quarry. In addition, the FSLN / KGB's drug facilities were also disguised as Banana and Coffee processing factories, and the Militaires Sans Frontieres also utilized an elaborate base in the form of an off-shore OTEC research facility.
 * The Ancients in (old verse) Might and Magic seems to have been fond of placing large facilities underground. The inhabitants of Deyja went one step beyond and built themselves an Elaborate Underground City.

Web Comics

 * In Narbonic, Narbonics Labs moved to an underground lair early in the strip's run. Later subverted when Madblood brags to Helen about his underground lair; when she and Mell come to visit, they find him living in his mother's basement.
 * Seems to be the basic design for all Orsintos laboratories in Sluggy Freelance. Surprisingly, there's been nothing so far to suggest that Hereti-Corp has one of these.
 * As it turns out,
 * The main characters of The Pocalypse have a base placed under a supermarket in a city.
 * Times Like This: It may technically be an Elaborate Underground Base, since it's run by a multination secret-service consortium, but Paratopia is actually an underground Club Med-type getaway roughly the size of Delaware.

Web Original

 * In the Global Guardians PBEM Universe, most of the Evil Overlords and Diabolical Masterminds have one of these. The most notable example might be TAROT's primary base in the United States. It is a multi-level complex located four stories beneath the Pentagon's lowest level, and is entered through a secret elevator located in that building. The fact that Federal law enforcement agencies would never think to tear the Pentagon apart looking for it amuses The Emperor greatly.
 * Pelvanida from Darwins Soldiers is an underground military research base. It is not really "hidden" per se, though as quite a bit of above ground infrastructure is present.

Western Animation

 * In a series full of Supervillain Lairs to begin with, in the Birdman episode ("Number One") that brought them into the open and really defined them as a threat, F.E.A.R. turned out to have an elaborate underground base.
 * In the Chip 'n Dale Rescue Rangers pilot, Aldrin Klordane had turned a cave conveniently placed underneath the Federal Gold Reserve into his own Elaborate Underground Base which not only has a diagonal monorail, but even a real railroad connection.
 * Danger Mouse lived in an underground base in postbox on Baker Street in London, the same road as Sherlock Holmes.
 * Vlad built himself one in Danny Phantom by the beginning of Season Three. Through an alternate universe, the underground base was a Foreshadowing element in a previous episode. Too bad he didn't find the time to put it to good use.
 * Dexters Laboratory, though how underground the lab is isn't really gone into, mostly due to physical impossibility.
 * Gummi Glen in Gummi Bears. This version distinguishes itself by its surprisingly realistic take of an underground structure of such extraordinary complexity in medieval times. Namely, the Glen requires a sophisticated infrastructure like a mechanical ventilation system to maintain air quality while the Gummis have a variety of maintenance concerns like water levels, plant growth and erosion of the surrounding ground.
 * Syndrome has an absolutely awesome underground base in The Incredibles, complete with the 50's-60's Tiki/Googie/Art Deco look. Egg shell people-movers, yeah!
 * Don't forget, it was built inside an active volcano!
 * Jackie Chan Adventures had the underground base of Section 13 in San Francisco. Said organization was where the main characters would live along with being the location of what ever MacGuffins were being collected that season. Could be reached via a phonebooth elevator or "the stairs".
 * Global Justice headquarters, and several of Drakken's lairs, in Kim Possible, which also has a twist on the trope: Frugal Lucre's lair in his mom's basement.
 * Also, a few of the locations that Drakken raids are themselves underground bases. Case in point, the episode where he steals some HypnoTrinkets had him raiding a base in the Cold Opening that was built underneath a desert, and a conspicuous Cactus acted as a card key scanning device to grant entry.
 * The Road Rovers had an Elaborate Underground Base. It was strongly implied in at least one episode that it was the remains of a lab in Socorro, NM, that the Rovers' mentor ran.
 * The Swat Kats have a base hidden beneath the Cool Garage where they live and work.
 * The Teenage Mutant Ninja Turtles live in a hideout within the sewers of New York City.
 * Don't forget about the Labrynth in Gargoyles.
 * Or the base Hacker dug out for himself in an episode of Cyberchase. He abandoned it by the next episode, though.
 * Jonny Quest TOS episodes "The Dreadful Doll" (arms and submarine base being built on the island), "Pirates From Below" (cave system with submarines and hovercraft), "The Fraudulent Volcano" (built under/in the title volcano).
 * In The Simpsons, wealthy businessman and supervillain Hank Scorpio has an underground base with some sort of nuclear-powered ray gun in it, plus a laser for cutting spies in half. It also has a snack vending machine with a touchy dollar bill acceptor.
 * Avatar: The Last Airbender: the Dai Li had a undergound base under a lake.
 * Perry The Platypus has one underneath Phineas and Ferb's house, and the rest of the OWCA base seems to run beneath all of the Tri-State area. All of it.

Real Life

 * Underground command-and-control centers started getting popular sometime after World War I, and much more so after nuclear weapons and ICBMs. Greenbrier Resort was the site of a US Congressional command center for 30 years, until a Washington Post reporter exposed its existence in 1992. Cheyenne Mountain, Colorado, is quite famous as the "brain" of NORAD (NORth-american Air Defense), SAC (Strategic Air Command, bombers and land-based ICBMs) and the US Space Command (more to do with satellites, though). The latter two are now defunct, absorbed into other organisations. NORAD is now based at Peterson Air Force Base (a conventional above-ground air force base nearby), but keeps Cheyenne Mountain on warm standby.
 * The famous Situation Room (yes, it really does exist) underneath the West Wing of the White House. Yes, this is where the President and his cabinet meet to make life-or-death decisions. No, it is not full of beeping computers.
 * Russia, ex-Soviet Union, undoubtedly has its own, but locations are disputed.
 * There's supposedly an entire secret subway system under Moscow, bigger than the regular one and buried up to 200m underground, linking numerous important buildings and providing means for movement and evacuation of VIPs.
 * Nobody in the West seems to know what's under Mount Yamantau, but whatever it is, it's definitely huge.
 * Similar to the Greenbrier Resort are the Canadian Diefenbunkers
 * A few shots in the movie War Games showed the actual Cheyenne Mountain complex. The NORAD room in that was a mock-up (the most expensive movie set ever at that time) and far more snazzy than the real one.
 * The Second-In-Command of NORAD is a Canadian (it's NORTH AMERICAN Air Defence, not American Air Defence) - and yet in all the movies set in Cheyenne Mountain there is nary a Canuck in sight.
 * Also, Cheyenne Mountain is in Stargate SG-1 and Jeremiah (This one has the benefit of being a real complex). In the original movie Stargate, the Gate was hidden in the fictional Creek Mountain complex -- also in Colorado, and to boot having recycled the Cheyenne Mountain entrance set from War Games. The series retconned the Stargate's location without much fuss.
 * Raven Rock, most famous to gamers from Fallout3, is a real base built for much the same purpose as Cheyenne Mountain.
 * Offutt Air Force Base is rumored to have an underground command center proof against anything short of a direct hit with a nuke. It's impossible to be certain, because those chambers are not on the Official Elementary School Field Trip tour, they're still in use. (George W Bush did not fly to Omaha on 9/11 because he wanted steak for lunch ....)
 * After the Cold War, the Strategic Air Command bunker in Amherst, Massachusetts was put up for sale. Who besides the government could want an elaborate concrete bunker? Librarians, apparently; the Five Colleges bought it for cheap, and now use it for book storage. The low temperatures and lack of sunlight are ideal for preservation, and it's hard to beat the security.
 * Speaking of decommissioned bunkers and missile silos, there's a [ specialising in such properties.
 * After the First World War, the French built the Maginot Line on their border with Germany, a chain of defensive fortifications connected by underground tunnels with bunkers and living facilities. It was an amazing feat of construction. And ever after, people have caricatured it by pointing out that the Germans went around it—which is true but misleading, because that was the purpose of the Maginot Line.
 * For contrast, Britain had Kelvedon Hatch Nuclear Bunker, a base for the nation's power structure hidden beneath a nondescript house. Apparently, it was active until 1992 (but only ever activated once: not for a nuclear crisis but for the poll tax riots). This site has pictures of it. It's now a tourist attraction and the real command centre is somewhere secret.
 * Has been used as a filming location.
 * Tourist signs directing people to it clearly say "Secret Nuclear Bunker".
 * London also had Churchill's Cabinet War Rooms under the Treasury building. Their existence was kept a secret until the 1980s, when they were renovated and opened as a museum.
 * The USSR had a secret underground submarine base on the Black Sea.
 * Iran is currently trying to protect their nuclear program by having the dedicated facilities be hidden in a series of tunnels.
 * The University of Illinois Undergraduate Library is entirely underground, save for two small entrances each about the size of a large trailer. It flies straight into Crazy Awesome territory when you find out they did this so that it would not cast a shadow on a nearby "historic" cornfield. Seriously, you can't make this stuff up.
 * In a similar vein, the University Library of the University of Stellenbosch, South Africa, was built beneath the central green, as the land was donated on the condition of the green being a recreation area for the students. A bonus is that the entrance is actually underground as well, as it is dug down into a sort of amphitheater. Emergency exits and aircon vents still pop up here and there, though.
 * The main stacks of Berkeley's central Doe Memorial Library take up about three stories below Memorial Glade (complete with skylights that are at ground level above).
 * The Cu Chi Tunnels in Vietnam are another great example, and are almost the archetype of the EUB.
 * The term "undisclosed location" entered the public lexicon after US VP Dick Cheney was stated to be touring them after attacks on DC and New York. Because of his reputation, it is somewhat assumed that any use of the term implies this trope played to the hilt.
 * Conspiracy Theorists speculate about the existence of DUMB, or Deep Underground Military Base. It doesn't sound any more sinister than your regular well-protected military base, except that it's supposedly run by your favorite conspiracy (The Illuminati and The Reptilians being popular choice) and people are abducted and carried there for unspeakable purposes.
 * Željava Air Base in former Yugoslavia is the world's largest underground Air Base. While they still have overground runways, everything else is underground and has enough food, fuel and ammo to survive 30 days without outside intervention. It has been, alas, demolished.
 * Julian Assange's Wikileaks facility in Stockholm.
 * It's just a web host. It doesn't belong to Assange.
 * It happens in private as well. In 2005, Fred Strunk was sentenced to 18 years for running an elaborate pot growing operation in a cave in Tennessee.
 * This datacentre in Sweden, located in a cold war era nuclear bunker.
 * In London, the underground railway linking Royal Mail facilities, now closed, but documented by urban explorers.
 * The North Korean military has a lot of bases created underground, some hollowed out from mountains to protect their equipment from bombardment in a future conflict involving South Korean and American bombing raids. The North Korean military also had several underground tunnels built so their troops could surprise-invade South Korea when the time is right.
 * Muammar Gaddafi, the former dictator of Libya, had a huge underground base hidden under Tripoli. Among other things, it contained an entire functioning hospital and stockpiles of food large enough for an entire city. It also had tunnels big enough to drive tanks through.
 * It is commonly speculated that Area 51 has a vast underground system where all the top secret research and technology development is made. From the surface there have been signs of hangers and Air Force bases but nothing truly out of the ordinary, this had led people to believe that there must be something underground they are hiding if the surface appears to be normal.
 * Humans don't have a monopoly on this trope either; ants have been known to form some fantastically complex underground structures. You think this one is impressive then the largest one know, under Hokkaidō, has an area of roughly 2.7 square kilometers.