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Anime and Manga
- Cyborg 009: An Island Base showed up in the first episode of the anime. It was used by two Mad Scientists like their Mad Scientist Laboratory.
- Mazinger Z. Big Bad and Mad Scientist Dr. Hell had two Island Bases: Bardos, an ancient Greek island full of underground mazes and labyrinths where he found an army of Humongous Mecha: and Hell Island, an island near from the Japanese coast where he moved later in the series. It was a barren, rocky islet. A low mountain rose in the center, and several giant faces had been carved on its slopes. The Dragon Baron Ashura also had an Island Base doubled like a Cool Ship: the submarine fortress Salude.
- Great Mazinger: Marquis Janus' Home Base was at once a Cool Ship (it was mobile and could swim or dive underwater), an Island Base (it was shaped like an island) and a Volcano Lair (an artificial volcano had been built in the center).
- Mewtwo from Pokémon: The First Movie. To add to the sinister atmosphere, it was built on the wreckage of the lab - where he was created - that he blew up a few months earlier.
- Wonder Woman and her race of Amazons live in a secret island.
- Oolong Island served as a think tank for a number of Mad Scientists in the DC Universe. It is now where the Doom Patrol are based.
- Monster Isle is the base of operations of the Mole Man in Fantastic Four
- The Teen Titans' Titan's Tower is on an island.
- Avengers Island, home base of the New Avengers, which was originally A.I.M.'s (it was probably called differently then) until Sunspot bought it. As in the whole organization. The island base was extra.
- It was originally Hydrobase, an artificial island originally stationed just outside of New York Harbor in the Atlantic. Once the base of operations of Sub-Mariner foe Dr. Hydro, it became the longtime home base for Dr. Walter Newell, the government operative Stingray. He later leased out space on the island to the Avengers for an airfield after the FAA banned them from flying their Quinjets through Manhattan, and it even served as their temporary headquarters after the Masters of Evil had trashed the original Avengers Mansion, until Doctor Doom's robots sunk the island. It was later salvaged by Namor and Stingray, and eventually relocated to the Pacific, off the coast of California, by the time Sunspot acquired it.
- A.I.M. previously had an island base simply known as A.I.M. Island. They later conquered the small Caribbean island of Boca Caliente. Tony Stark tried to get the US government to liberate Boca Caliente from A.I.M., to no avail.
- Cobra had a temporary island base in the first issue of G.I. Joe: A Real American Hero, and later gained a larger and more permanent one in international waters in the Gulf of Mexico by having the Joes help them create it. Specifically, they tricked the Joes into detonating a fault line at just the right location to cause enough upheaval to create the island. Cobra even had an army of laywers standing by at the UN to lay their sovereign claim to the newly-formed Cobra Island. It serves as the focal point for several stories, including the original Cobra Civil War.
- In The Transformers, Shockwave had the Decepticons construct an artificial island base off the coast of Florida, the surface of which concealed the fact that it was also a fully-functional space cruiser. Ratbat later turned the island into a vacation resort called Club Con, even going so far as to having Starscream appear in a television commercial for the resort. The base/ship was destroyed when the Underbase-empowered Starscream crashed Scorponok's ship into it.
- Dungeon Keeper Ami features several- all of which score bonus points for covering the active volcano, skull-shaped cave, and so on. Just not all at the same time. Zarekos' Islands were riddled with lava-filled fissures, due to the tremendous dark energy contamination, which Ami inherited from him, following his deafeat. Ami, naturally repurposed them for use as geothermal plants. Later, the battle of Dreadfog Island takes place on an island in a large swamp- and the island sports a skull-shaped cave incorporated into the fortifications.
- Soul Eater: Troubled Souls: Cobra Island acts as one for Medusa in the titular Story Arc. She is huddled up in the snake monolith that takes up most of the island. It is also her place of birth. She's dragged Maka and the others to the island to enact the beginning of a revenge scheme.
- Most notable examples are with James Bond villains.
- Dr. No's Base was on Crab Key, albeit more of an Elaborate Underground Base.
- You Only Live Twice. Blofeld's rocket base is under an extinct volcano on the Japanese island of Matsu.
- Blofeld held headquarters on an oil rig in Diamonds Are Forever, technically an island.
- Kananga's island of San Monique in Live and Let Die, but it isn't really isolated: it has a tourist trade. Too bad - poppy fields, voodoo totems with guns, Baron Samedi, and a Shark Pool.
- Francisco Scaramanga's private island is probably the best example of the trope in The Man with the Golden Gun.
- Stromberg's Atlantis base in The Spy Who Loved Me was a giant floating platform.
- Silva's island in Skyfall used to be inhabited, until he faked a chemical leak, causing the inhabitants to evacuate.
- Dr. Totenkopf's island base in Sky Captain and the World of Tomorrow (2004), complete with robots, prehistoric animals and a space ship.
- Our Man Flint. Galaxy Island is the headquarters of the Galaxy organization. Features include brainwashed women, a Weather-Control Machine and an anti-American eagle.
- Captain Nemo's island headquarters in the Disney version of Twenty Thousand Leagues Under the Sea. Volcanic crater, submarine docking facilities and Self-Destruct Mechanism.
- Yellowbeard. El Nebuloso's island, with a castle full of murderous monks.
- The Nazi-controlled island in Raiders of the Lost Ark. Submarine docks, and an area where you can perform Jewish rituals. Watch out for exploding heads.
- Baron von Frankenstein's island in Mad Monster Party. He has a castle where he performs bizarre experiments.
- Undercover Brother. The Man (head of a white racist organization) has his secret fortress built on an island.
- In the Austin Powers series, Dr. Evil once held operations inside a volcano shaped like his head which was key geographical icon on a Caribbean island.
- Spy Kids 2 had an island with a hidden base inside the volcano, and gengineered monsters running around.
- Jurassic Park. The eponymous amusement park is built on an island, Isla Nublar. The Lost World: Jurassic Park reveals the primary research facility was on a separate island, Isla Sorna.
- Black Dynamite faces foes on both Kung-Fu Island and Slave Island.
- Jurassic Park, justified as they need it contain all the dinosaurs. Unfortunately it's not as secure as they think.
- Most of Billy & Howard and Duumvirate take place on one of these.
- "Lincoln Island" is the headquarters of Captain Nemo and the harbor of the Nautilus in The Mysterious Island.
- In The Island of Doctor Moreau by H.G. Wells, the eponymous island, where Dr. Moreau performs his experiments with human mutation.
- In The 39 Clues universe: the Ekaterinas had a island base inside the Bermuda Triangle.
- The Madrigals have Easter Island as a base.
- There's also the Cahill ancestral home and the Gauntlet, on an island off the coast of Ireland.
- In Soon I Will Be Invincible, Dr. Impossible used the same island base for 14 years before the heroes finally cracked it. At the climax of the novel, he returns to construct his new Doomsday Device in the ruins.
- The Most Dangerous Game. General Zaroff has Ship-Trap Island, where he passes the time hunting humans.
- In Warrior Cats, RiverClan makes camp on an island. That is until they are forced to move out of the Old Forest and travel to the lake, where they get a new, not-really-islandy camp. But they make up for it in Dark River when they take over the Gathering Island due to their current camp being unavailable to them.
- Swellhead. The protagonists are sent to investigate strange events on the long-deserted and distant island of Skerra, somewhere on the ill-defined border between Britain and Ireland which for historical reasons even has a monarchy (not that she's ever set foot on the island before now) and is therefore an independent nation. Turns out an Elaborate Underground Base has been discovered on Skerra, despite the sheer impossibility of constructing one without vast resources and public knowledge. One which, as they delve further into it, looks increasingly like a classic Supervillain Lair... It turns out the base was constructed by a supervillain in an Alternate Universe, which is encroaching into our reality.
- Goro Yoshida, the eponymous villain in The Man with the Red Tattoo has set up camp for his private nationalist army in Etorofu, which is one of the Kuril Islands, which reside in a disputed territory between Russia and Japan.
- The Dresden Files: From Cold Days on, Demonreach has become this for Harry. It's secluded location and powerful Genius Loci make it far more defensible than his old apartment, but at the same time more vulnerable, as the island is the site of a massive supernatural prison constructed by the original Merlin to hold some of the baddest bads in the setting, and some of Harry's enemies are interested in setting those baddies loose. The isolation from his friends and allies his relocation to the island has caused is also a minor plot point.
- Mystery Island serves this purpose for Cobra in Secret Agents Four.
Live Action TV
- Adventure The Island of Doctor Destroyer. The title island Destruga holds the secret base of Doctor Destroyer, from which he plans to launch the Hypnoray satellite and Mind Control the entire world.
In Classic Organizations, after being destroyed in its original location Neutral Ground relocates to this exact island, turning from a fairly posh club for supers of all kinds into an island resort in the process. Doctor Destroyer's legacy is brought up in the relevant chapter and used as a plot point in at least one example adventure outline.
- The Champions II supplement has rules for constructing superhero bases. When choosing a base's location, one option is to build it on an island.
- Adventure The Island of Doctor Destroyer. The title island Destruga holds the secret base of Doctor Destroyer, from which he plans to launch the Hypnoray satellite and Mind Control the entire world.
- GURPS Illuminati. One potential location for the Illuminati main base is on a private secret island that has been erased from the world's maps. It could even be in the Bermuda Triangle - the reason so many ships and planes have disappeared there is because they got too close to the Illuminati base and saw something they weren't supposed to see.
- Hollow Earth Expedition. If a character has the Resource of Refuge 5 they have a secret island base with everything they could want.
- The Nazis have two of these. Since Space Is an Ocean they've built one on Mercury and one in the asteroid belt. Festung Sieg on Mercury. The other is built into one of two asteroids attached to an Erisian spaceship wreck.
- Fur Fighters has the last level set in a James Bond parody Island base...just off the coast of your hometown.
- Mega Man Battle Network 3, the WWW has their base on an island, across the Demon Waters.
- Metal Gear Solid
- Shadow Moses Island is indeed an island - something the players (and at one point even Snake) needed to be reminded of.
- Metal Gear Solid: Peace Walker's Mother Base can become this with time.
- In Phantom Brave, Marona lives on an island all to herself, called Phantom Isle, which she uses as a base. The Big Bad, Sulphur, also has an island of his own, called the Island of Evil, which he is sealed in.
- 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.
- In The Curse of Monkey Island, King André operates out of Skull Island. Subverted in that Skull Island really looks like a giant duck;s head, prompting Guybrush to complain "It should be called Duck Island!"
- Evil Genius goes for a twofer, having you tunnel into the mountain on your "Uninhabited Desert Island of Undisclosed Location (tm)". Midway through you're forced to move islands, because if you're going to use satellite-based doomsday weapons it's obligatory to launch them out the crater of an extinct volcano.
- In Knuckles Chaotix, Dr. Eggman builds his latest Supervillain Lair on an island in order to get himself one step closer to several Chaos Emerald-like objects rumored to be hidden there.
- Used and Lampshaded in Kingdom of Loathing; after your Nemesis pulls a Villain Exit Stage Left after your first battle with them, your class leader says they probably have a secret tropical island volcano lair. Sure enough, you eventually find a map to a secret tropical island volcano lair on one of your Nemesis's thugs and have a final showdown in the heart of the volcano, first with your Nemesis's normal form and then with its Demonic form. Troperrific!
- Red Alert 3 features a secret island base. A secret Easter Island base. In a volcano. With cannons in the Heads. That shoot bears.
- Dr. Nonookie's Nontoonyt Island lair in Leisure Suit Larry II.
- The headquarters of Cipher, Citadark Isle, in Pokémon XD: Gale of Darkness. They even have a machine that generates a constant storm around the island to prevent any unwanted visitors.
- The game Device6 takes place on a seemingly abandoned one of these.
- Legend of Hero Tonma takes place on one named Untrodden Island.
- Governor's Island serves as the headquarters of Soviet forces occupying New York in Freedom Fighters. Two missions revolve around it, one to infiltrate it and assassinate General Tatarin and the final mission where it is stormed en masse by boat.
- In both Rymdjakten (The Space Hunt) and Djuphavsjakten (The Deep Sea Hunt), the heroes are headquartered on an island solely owned and inhabited by them. They start out rather mundane, with just the home of the person(s) who discovered the central issue of the game and some kind of facility relevant to the game (an observatory in Rymdjakten, a lighthouse in Djuphavsjakten), but by the later portions they include, among other things, training facilities (for astronauts in Rymdjakten, and for divers and dolphins in Djuphavsjakten), construction facilities, laboratories, and in Rymdjakten two rocket launching pads. In both games, all of this is privately owned.
- The Island of Claymodo in ''Clayfighter 63 1/3", home of the Mad Scientist Dr. Kiln.
- During the spy spoof arc of Dan and Mab's Furry Adventures , Dr. Jyrras' base is an island with an extinct volcano. Filled with orange pillows to simulate lava. It's supposed to be incredibly secret, but the agency has detailed plans.
- Subverted in Sluggy Freelance:
Dr. Steve: It was your mistake to trespass on... [Dramatic Pause]... the Isle of Doctor Steve!Torg: "Isle"? We're in the woods. I never left the mainland!Dr. Steve: Do you know how expensive islands are these days?
- Narbonic: The happy ending has this for Helen (and Dave, by extension).
- Villain Source (formerly Villain Supply) has options of either a Skull Island or a subterranean base on a volcano island.
- KateModern Big Bad Michelle Clore's evil lair is located on (Real Life) Adak Island.
- At the beginning of episodes of the Dr. Steel show, Doctor Steel's secret laboratory is shown to be on an island. Supposedly this island is located in the Pacific, near Hawaii.
- Cobra Island in G.I. Joe: A Real American Hero was introduced in the two-part episode "There's No Place Like Springfield", where the titular town was staged for a Faked Rip Van Winkle plot to get Shipwreck to reveal a top-secret formula he'd been entrusted with. In the second season, it became Cobra's permanent base of operations with the completion of the Terrordrome.
- Dr. Drakken and the Seniors both have island bases in Kim Possible. The Seniors' island was originally just their home, but Ron kept comparing it to a typical Supervillain Lair, inadvertently giving Seńor Senior, Sr. the idea to take up supervillainy as a hobby. It didn't help that the ginormous sunlamp for Seńor Senior, Jr. had been causing blackouts across mainland Europe, which is what brought the Seniors to Kim and Ron's attention in the first place. Drakken has several other lairs, but most of them seem to be temporary, as he keeps coming back to his island base.
- Science Island is the headquarters for Jarvis Kord in Batman: The Brave and the Bold.
- The bunny-shaped island known as Bunny Island is the primary setting for Evil Con Carne.
- Jonny Quest TOS. Dr. Benton Quest's island of Crab Key. It had dock facilities, experimental labs and a hovercraft.
- Phineas and Ferb. Doctor Destructocon (Kevin to his friends), one of Dr. Doofenshmirtz's mentors, had a secret-hideout shaped island with the letter "D" carved into it.
- Prometheus Black AKA, Meltdown has a underground lab on Dinobot Island in Transformers Animated. Blackarachnia moves into it later in the series. Apparently it used to belong to the government.
- The Legend of Korra has Air Temple Island◊ where Tenzin and his family live.
- Super Friends episode "Too Hot To Handle". Kobar the Solar-Terrarian villain has his laboratory hidden under a volcano on an island.
- Young Samson & Goliath episode "The Secret of Evil Island". The Big Bad Voltor has his base on Evil Island, which is just off the coast of New Guinea. From there he imitates Doctor No by hijacking satellites and using their fuel to power his city/continent destroying missiles.
- Principality of Sealand: A small former UK military installation used by various groups for a number of different purposes — from pirate radio station to server room. Declared an independent sovereign state at one point by the owners, which is taken seriously by absolutely nobody.
- World War 2 involved a lot of these, which include:
- The Hawaiian Islands, specifically Oahu and Pearl Harbor
- Fort Drum (AKA the concrete battleship) in Manila Bay
- The Channel Islands
- Malta (its refusal to surrender to the Axis was a constant pain for Italian and German efforts to keep their forces in North Africa supplied)
- Singapore (Winston Churchill called its loss to the Japanese in just one week the worst disaster in British history)
- Iwo Jima
- Possibly Japan and Britain on a large scale (see also below)
- During the Cold War, several U.S. allies acted like these as they hosted US military personnel; most notable were (and still are) the UK and Japan as they are actual islands, as well as Iceland (which didn't and still doesn't have a military when it joined NATO) and Taiwan (prior to the establishing of diplomatic ties between the US and China in 1979). Islands need not be purely geographical, either - Alexander Haig, Secretary of State under Ronald Reagan, called Israel the US's largest unsinkable aircraft carrier in the Middle East.
- Chagos Archipelago
- It houses a massive US military base at Diego Garcia. It was used for reconnaissance in the 1973 Arab-Israeli war and saw wartime use in the first Gulf War. After 9/11 it was key to the wars in Afghanistan and Iraq. It may house nuclear weapons and may be a "black site" for detaining prisoners. It is more secretive than Guantanamo Bay - which is probably why most people have never heard of it.
- In a true supervillain fashion, forty years ago, its people, the Chagossians, were unceremoniously removed from their homeland by a joint operation of the United Kingdom and the United States, and essentially left beached in Mauritius as human detritus. This was detailed in David Vine's book Island of Shame: the Secret History of the US Military Base on Diego Garcia.
- Not exactly at sea, but during The American Revolution, Francis 'Swamp Fox' Marion had a base on an island in the middle of the South Carolina swamps. It's depicted in the Disney series from the '60s as Snow Island.
- Haulbowline, which started as a British army base, then became a naval base. Today, the island is home to the Irish Navy.
- Mobile offshore bases are a proposed idea of combining this trope with Base on Wheels (we suppose it'd then be a Base On Hulls) so as to be able to extend force projection far beyond one's own shores (i.e., the US's) while still remaining in international waters and thus avoid a lot of political problems associated with (American) bases and personnel stationed overseas (e.g., Saudi Arabia, Okinawa).