- In X1999, The Dragons of Heaven have their headquarters under the Diet Building, while the Dragons of Earth reside under the Tokyo Government offices.
- Read or Die has its network of superspies based in a secret underground lair beneath the British Library. Justified in that they also work for the British Library.
- Digimon Tamers used several floors of the Tokyo Metropolitan Government Building as HQ for HYPNOS.
- The DCU:
- The All-Purpose Emergency Squad (APES) from Young Justice had its headquarters inside Mount Rushmore.
- The Quorom, an all purpose evil organization, had one of its main bases under the Reflecting Pool in Washington, D.C. (and a villain containment pod under the Washington Monument). Not quite a good idea when heroes smash in through the roof.
- In The League of Extraordinary Gentlemen, the League's headquarters is inside the British Museum.
- Marvel Universe:
- Possibly Avengers Mansion, which is based on (but not confirmed to be) Frick House, a museum in Manhattan's Upper East Side.
- Luke Cage operated out of an apartment above the (fictional) Gem Theater, near Times Square.
- In Superior Iron Man, while visiting San Francisco, Tony Stark built himself a futuristic base on Alcatraz Island. The X-Men also temporarily had a base on Utopia, an asteroid that crashed into San Francisco Bay.
- Spider-Man temporarily operated off of The Raft, a former prison on Riker's... uh, excuse me, Ryker's Island.
- The Weird Happening Organization in Excalibur had their offices inside the Tower of London, but it seems not to have been a secret, since a Yeoman Warder identifies some of the top operatives to some tourists rather offhandedly. note
- The Runaways second "Hostel" is an Elaborate Underground Base underneath the La Brea Tar Pits; it used to belong to their evil parents.
- Mr. Majestic, Wildstorm's Alternate Company Equivalent of Superman, has his headquarters inside (where else?) Mount Rushmore.
- Which makes their neighbor the teenaged antihero Anarky as he has his base of operations in the Washington Monument.
- A Fantastic Four tie-in novel had a supervillain (The Mad Thinker) craft a base in Mount Rushmore. Cue Reed sliding out of a nose. In the regular Marvel Universe, Mount Rushmore just tends to get blown up. Yes, more then once.
- The All-Star Squadron was based in the Trylon and Perisphere from the 1939 New York's World Fair. The Perisphere was their headquarters, and the Trylon was their Cool Garage.
- In Peter David's SpyBoy, the "good" spy team S.H.I.R.T.S. (Secret Headquarters International Reconnaissance, Tactics, and Spies) had their invisible headquarters suspended between the tops of the twin towers of the World Trade Center. (This got moved later, for obvious reasons.)
- In Invincible spinoff Guarding the Globe, Cecil shows team leader Brit around a new Guardians of the Globe satellite base — inside Big Ben. Brit isn't sold on the idea, and Cecil suggests having the Sphinx hollowed out to make room for a base there, too, maybe with a jet hangar. Brit can't tell if he's joking or not. He wasn't; a couple of issues later it's revealed that this is exactly what he did.
- In Spyman, a short-lived title from Harvey Comics in the 1960s, the eponymous hero worked for the secret spy organisation LIBERTY who were headquartered inside the Statue of Liberty.
- In Hex, the Batman of the future had his secret base inside the Statue of Liberty. Granted in the post-appocalyptic future, it was probably no longer a tourist attraction, but it was still definitely a landmark.
- G.I. Joe: A Real American Hero (Marvel): The Joes have secret base that controls a Kill Sat hidden inside the Chrysler Building.
- In the earliest issues of Marvel's Alpha Flight, the super-secret Department H and their team of Canadian superheroes are headquartered directly beneath the Parliament buildings in Ottawa. Apparently we WANT supervillains to regularly blow up the historic seat of Canada's government, located on the busiest street in downtown Ottawa.
- Wynonna Earp: Black Rock, the top-secret containment facility for paranormal threats, is hidden inside Mount Rushmore. In this case, Mount Rushmore was constructed specifically to hide Black Rock.
- In Neither a Bird, nor a Plane, It's Deku! a Villain has set up a base inside Mt. Fuji, one of Japan's most famous landmarks, by Chapter 5. Coincidentally, it's where Izuku's spaceship happens to be hidden.
- In 1978's Superman: The Movie, Lex Luthor is hiding in a defunct wing of the DC equivalent of Grand Central Station. This example is unusual in that the police actually suspect Luthor's presence in there, but one detective is mowed down by a train when he gets too close.
- Team America: World Police has the base in Mount Rushmore again.
- The villains in North By Northwest have a house on Mount Rushmore's peak.
- Austin Powers
- Transformers Film Series
- In National Treasure 2: Book of Secrets the ancient mythical city of Cíbola was hidden behind Mount Rushmore. Or rather Mount Rushmore was created to hide Cíbola.
- The huge movie studio in The Truman Show was behind the Hollywood Sign.
- Of course, there's nothing hidden about it, given that it's a gigantic dome clearly visible from space.
- Q: The Winged Serpent nests in the top of the Chrysler Building in New York City.
- CONTROL headquarters was under the Smithsonian Castle in Get Smart. Inside an exhibit about CONTROL itself (which the exhibit claims was disbanded at the end of the Cold War), no less.
- The Man with the Golden Gun: The wreck of RMS Queen Elizabeth is used as an MI6 base.
- The Return of Captain Invincible: Captain Invincible had a hidden base in the head of the Statue of Liberty... when he wasn't drunk off his mind in the Australian outback
- In the 1995 Judge Dredd film, Rico's secret cloning lab is located in the head of the Statue of Liberty.
- Part of the backstory for Star Gate is that the Pyramids of Egypt were built to be landing pads and support facilities for Ancient Astronauts and their massive starships. The only pyramid we actually see being used for this in the movie is on the planet of Abydos, in the Kalium Galaxy.
- The end of Now You See Me 2 reveals that The Eye has its headquarters inside Greenwich Observatory.
- In Mechanic Resurrection, an Arms Dealer has somehow turned the Buzludzha Monument in Bulgaria into a submarine pen.
- In the Doc Savage novel World's Fair Goblin, the villain has his secret lab hidden inside the Trylon and Perisphere at the New York's World Fair.
- Doc himself lived on the top floor of the Empire State Building, although this wasn't a secret base. It was public knowledge.
- Kim Newman's pulp homage/parody character Dr Shade apparently lives in a "secret" apartment in Big Ben. Since in Newman's world he's both a real adventurer and a magazine character (in a sort of takeoff of the Literary Agent Hypothesis), readers of the magazine wonder why it's described as secret.
- Arsène Lupin's base in the Hollow Needle happens to be inside the Étretat Needle, a natural landmark of the Seine-Maritime.
- In The Extraordinaires, the Immortals lair was beneath the Royal Observatory at Greenwich. Justified in that being at the prime meridian granted the location mystical significance.
- In the Percy Jackson and the Olympians series, Olympus is located above the Empire State Building, accessed via the elevator. Justified in that it's there precisely because the Empire State Building is so famous.
- In the Alcatraz Series, our hero needs to infiltrate the Highbrary, the capital and ultimate base of the Evil Librarians, in order to bring his Love Interest out of her coma. It is, naturally, located directly under the Library Of Congress.
- In Brown Girl in the Ring, Toronto crime lord and obeah man Rudy has his offices in the main pod of the CN Tower.
- In the President's Vampire series, Cade's lair is in a secret chamber underneath the Smithsonian Castle.
Live Action TV
- Stargate SG-1 had the Stargate under Cheyenne Mountain Air Force Station, which was the real-world home of NORAD. NORAD has since moved to Peterson Air Force Base, but the Cheyenne complex is kept on warm standby.
- Justified up the wazoo by the fact that this is an actual military base, so sticking a military base in it is hardly surprising.
- There's supposedly a door in the actual base marked "Stargate Command", though noone seems to have a key for it...
- There really was such a door and it was a broom closet.
- Sure it was.
- Neil Gaiman's Neverwhere has an entire culture of "lost" people and things inhabiting the various stops of The London Underground.
- Averted in Roswell. For some reason, the government keeps alien spaceships in secret basements under convenience stores, and in movie studios.
- Buck Rogers in the 25th Century had a second season episode in which Buck was accused of having helped foment the big nuclear war in the late 20th century. A device to visualize Buck's memories seems to confirm his guilt, but he keeps flashing on Mount Rushmore. Buck manages to get to Mount Rushmore and finds that the President had a secret bunker inside. It turns out that Buck had been to the secret bunker where he was hypnotized to act as a double agent as part of a government operation to catch the conspirators who were trying to start the war.
- The Canary Wharf Tower one was done by the 90s remake of The Tomorrow People. The reasoning was that the immortal Egyptian villain needed to hide a power-focusing pyramid in the middle of London, hence the pyramidal top of the tower.
- The notorious Belgian mockumentary Bye Bye Belgium (a Flemish secession hoax reminiscent of Orson Welles The War of the Worlds broadcast) at one point reported the Brussels government holding an emergency meeting in a fictitious underground tenth ball of the Atomium.
- The Torchwood Institute has had bases:
- In One Canada Square (a.k.a "Canary Wharf Tower") in "Army of Ghosts"/"Doomsday".
- Under the Thames Barrier in "The Runaway Bride", where it's lampshaded:
Donna: What, there's like a secret base hidden under a major London landmark?
The Doctor: I know! Unheard of...
- Under Roald Dahl Plass, near the Millennium Centre in Cardiff, where The Hub is based in the Whoniverse spin-off Torchwood (and in "Utopia", "The Stolen Earth" and "Journey's End").
- UNIT has one: Under the Tower of London in "The Christmas Invasion" (revisited in "The Power of Three" and "The Day of the Doctor"). It beat their early place that had a conspicuous "Keep Out" sign.
- In Big Finish Doctor Who audio dramas, UNIT's top secret Museum of the Strange and Unusual, "the Vault", is under the Angel of the North. Lampshaded when Captain Matheson says "You thought we only had bases under London landmarks?" "The Day of the Doctor", however, Retcons it to be under the National Gallery in London instead - which was then duly retconned again by Big Finish who stated that obviously you sometimes need two archives to keep certain exhibits apart from each other. So according to this, UNIT has both the Black Archive under the National Gallery and the Vault under the Angel of the North. The Screaming Skull which establishes this, also claims that the Vault predates the Angel of the North, but UNIT was uncomfortable having a secret base not under a landmark, so they arranged to get one!
- Various bad guys have based themselves in/under:
- Gatwick Airport (The Chameleons in "The Faceless Ones")
- The Post Office Tower (WOTAN in "The War Machines")
- The London Eye (The Nestene Consciousness in "Rose")
- The Empire State Building (The Cult of Skaro in "Daleks in Manhattan"/"Evolution of the Daleks")
- Trafalgar Square (Operation: Golden Age in "Invasion of the Dinosaurs")
- Stonehenge (The Pandorica in "The Pandorica Opens")
- The Shard (The Great Intelligence in "The Bells of Saint John")
- Battersea Power Station (The Cybermen Factory in "Rise of the Cybermen" and "The Age of Steel")
- St Paul's Cathedral ( The 3W facility/Cyberman factory in "Dark Water" and "Death in Heaven")
- They make an attempt to justify many of these, explaining there is something important about the location or nature of the structure that they need. For example, the Torchwood Tower (Canary Wharf) exists because there was a rift high in the air, so they had to build a giant tower to reach it, The Hub's location was chosen due to its proximity with yet another rift and the Nestene Consciousness was using the London Eye as a giant transmitter to broadcast the signal controlling the Autons. In "Daleks in Manhattan", the Daleks attached Dalekanium strips to the top of the Empire State Building (which at the time was the tallest building on Earth) to kick-start a new race of hybrids with a solar flare.
- Canary Wharf is also the headquarters of the British time travelling military in an alternate 2006 visited by the First Doctor in the Past Doctor Adventures novel The Time Travellers. And the villain fought by the Sixth Doctor in the Doctor Who Missing Adventures novel Millennial Rites (for reasons broadly similar to the Tomorrow People villain).
- In Tom Clancy's Rainbow Six: Vegas, a top-secret Army Weapons Research Lab is located inside the lower levels of the Hoover Dam, which contains numerous highly dangerous weapons and vehicles. Why they just didn't do the research at nearby Area 51 isn't explained.
- Similarly, in Tom Clancy's Ghost Recon: Advanced Warfighter 2 apparently a computer system linked to the United States anti-ballistic missile defense grid's mainframe is located under a dam in El Paso Texas.
- Nearly everything in Fallout 3, since the game takes place in Washington, D.C. After the End. The most recognizable are probably the Washington Monument (Brotherhood of Steel and Three Dog's communications relay), the Pentagon (Brotherhood of Steel), the Mall and Museum of Science (Super Mutants), Museum of History (Ghouls), the Jefferson Memorial (Project Purity), the Lincoln Memorial (Slavers and eventually freed slaves), the ruined Capitol Building (in some ways the Bonus Dungeon), and the White House Crater.
- Justified with the Pentagon and the Lincoln Memorial. The Brotherhood chose the Pentagon both because it was easily defensible and because it contained plenty of pre-War technology (including Liberty Prime). The slavers don't want slaves to be exposed to anything related to Abraham Lincoln.
- In Deus Ex, UNATCO's HQ and therefore a major MJ12 facility are both built on Liberty Island.
- This one is justified in game as a symbolic decision. UNATCO was founded in response to a terrorist attack that destroyed the Statue of Liberty.
- S.T.A.L.K.E.R. is all about the terrible secret at the center of the Zone of Exclusion, buried deep within the Chernobyl Nuclear Power Plant. Conspiracy Theorists might also get a shudder at the inclusion of the Duga-3 Over-The-Horizon-Radar array's inclusion, known in Number Station circles as the Russian Woodpecker, suspected by some as being a Mind-Control Device or Weather-Control Machine. In the series, it does both. Not to be confused with the Brain Scorcher from the first game, which is merely based on the Duga-3.
- In Evil Genius, a rival genius tried to build an underground lair inside the Great Wall of China, consisting of a single corridor.
- Earthbound has a secret lab underneath Stonehenge.
- Devil Survivor 2 has the JP's headquarters located right underneath the Diet Building in Tokyo.
- In the Nasu Verse, the headquarters of the Mage's Association is located under the British Museum, despite being referred to as the Clock Tower.
- Due to the nature of the surface of post-apocalyptic Moscow in Metro: Last Light, this is not a common trope, but it hasn't stopped the Rangers from establishing an outpost in the ruins of St. Basil's Cathedral. Meanwhile, the Rangers' home station of Polis is located directly beneath the Moscow State Library.
- Though they maintain more conventional safehouses, The Chain in Necessary Monsters maintains a base under the Statue of Liberty called Liberty's Price. It's a huge cavern with occult symbols, and an inverted, chained, tortured version of the Statue of Liberty as its centerpiece. However, Liberty's Price is implied to be older than the landmark built over it.
- Ben 10 has The Plumbers base be inside the ever-popular Mount Rushmore. It's been destroyed more than once, but holograms are used to hide the damage.
- In one episode of Phineas and Ferb Dr. Doofenschmirtz has a hidden base inside Lincoln's head at Mount Rushmore.
- In Spider-Man: The Animated Series, the Kingpin's lair is in the Chrysler building. There's a secret underground entrance so people not in the know won't find out where his base is (even though the lair's high ceiling looks like the interior of the Chrysler Building's spire might be expected to look). Of course, five seasons later, enough airborne bad guys have waltzed in and out that someone oughta suspect that something about that nice philanthropist Wilson Fisk isn't kosher.
- Parodied on The Venture Bros. The Monarch brags about how his base is in such a secret location that he flies by radar alone to get there, that it could be anywhere and nobody would find it...except that it's in the Grand Canyon and very visible.
- Parodied on The Simpsons. In one "Treehouse of Horror" episode, a missile launch pad is under the Eiffel Tower.
- The indie computer-animation short Pigeon: Impossible has a pigeon accidentally fall into a CIA agent's briefcase, activating a Big Red Button that launches a nuclear missile out of the Washington Monument.
- Batman: The Brave and the Bold: In "Darksied Descending!", it is revealed that Batman has an auxilary Batcave located under the Lincoln Memorial.
- Totally Spies!: Whoop's European HQ is located underneath the Effiel Tower.
- The White Cliffs of Dover hide a network of formerly secret underground tunnels.
- Gustave Eiffel built a private apartment for his own use on top of the Eiffel Tower in Paris.
- Similarly, Walt Disney had a secret apartment within the iconic castle in the heart of Disney World.
- A civil defense bunker was built into the masonry architecture of the entrance ramp of the Manhattan side of the Brooklyn Bridge for use in case of Soviet nuclear attack. It was then forgotten about until a routine inspection came across it by accident in 2006, still stockpiled with blankets (marked "For Use Only After Enemy Attack") and cookies. Such bunkers and shelters were ubiquitous in cities across the US when nuclear attack was an everyday concern, but most were cleared out and closed down with the end of the Cold War.