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- UFO Robo Grendizer (one of the Mazinger Z sequels: The lair of the Vegan invaders was a Space Base set in the Moon they used to launch their raids and strikes from. When the Emperor began his final offensive against Earth, he ordered blowing it up to show his troops they had only two choices left: conquering Earth or die.
- Precia Testarossa has her base in a different dimension. In space.
- The bad guys in Nurse Angel Ririka SOS operate out of a weird starfish-shaped asteroid-thing that seems to be in Earth's orbit. It's in space at any rate.
- DC Comics' Injustice Gang had a satellite space station hangout at one time.
- DC Comics' Legion of Super-Heroes has had a couple of these at different points. In the post-Zero Hour continuity, they built Outpost Allon, a space station which served as a secondary base. And later, after the Outpost was destroyed, they built a moon-sized Space Base called Legion World to serve as their (mobile) base of operations.
- In X-Men, Magneto has the Asteroid M at first, and then Avalon.
- In All Fall Down, the Order of Despots has one of these on the moon. It's seen in first in a flashback, and is later visited in the present.
- Suverted in a Biggles comic where the space station armed with nuclear weapons to blackmail the world turns out to be an inflatable hoax.
- The Justice League has the JLA Satellite, orbiting Earth, both in the 70s, (the Satellite Era) and in the New 52. In the late 90s-early 2000s, they also had the Watchtower on the moon.
- Simon Tycho, the first supervillain faced by Supergirl in the New 52, had a Space Base. Had being the correct word, it's quickly destroyed by Kara.
- The headquarters of the Black Moon religion in the Black Moon Chronicles is located on the moon and accessible only via magic (the series is essentially an old Dungeons & Dragons campaign of the author's). The Big Bad sends it crashing onto the planet on his defeat, forcing the heroes to evacuate as many people as they can onto a different planet.
- The film version of the James Bond story Moonraker has its climax take place in a orbital space station.
- The second Austin Powers film also has a moon base, complete with moon laser.
- Star Wars: If examples where everything's in space count, then we wouldn't be complete without mentioning the Death Star, a moon-sized space base capable of blowing up whole planets.
- Transformers: Revenge of the Fallen has the Fallen's base/pad/hatchery on a moon of Saturn.
- In Iron Sky, an exiled faction of Nazis control a moonbase since leaving Earth in 1945.
- In Elysium, a few wealthy people live in luxury on a space station, while everyone else lives in poverty on Earth. While those on Elysium are less moustache-twirlingly evil than most of those with villainous lairs, the film certainly portrays them as the bad guys for refusing to help despite having the technology and resources to do so.
- In Dragons Lexicon Triumvirate, Drekkenoth has one on the moon, of course. It's the scene of the final showdown. Also, the dragons all ''fly'' from Earth to the moon base. In, quote, "less than five seconds".
- Robert A. Heinlein novels:
Live Action TV
- Inverted in Gerry Anderson's Space Precinct where the police precinct house is a space station. Of course, this doesn't make much sense, but it's supposed to look cool.
- Kyoryu Sentai Zyuranger- Bandora's palace is on the moon. Same naturally goes for Rita Repulsa in Mighty Morphin' Power Rangers.
- A nonvillainous example in Kamen Rider Fourze. The protagonists can access a lunar research base (dubbed the "Rabbit Hatch") via Kengo's locker (which contains a passageway made of Cosmic Energy). It becomes the hideaway for the Kamen Rider Club which is then littered with toys, food, and other paraphernalia to suit the teenagers' needs.
- The Operative: No One Lives Forever had HARM's space base as one of the last levels. Since the game is largely a parody/homage of the classic Spy Fiction, it's safe to assume that that level was at least partially inspired by the Moonraker.
- In the old arcade game Captain America and the Avengers, Red Skull has a moonbase, complete with giant laser cannon.
- A related video game / comic example: Asteroid M, for Magneto.
- The X-Nauts in Paper Mario: The Thousand-Year Door.
- Team Fortress 2 has Asteroid.
- Super Mario Galaxy has Bowser Jr's Robot Reactor, Bowser's Star Reactor, Bowser Jr's Airship Armada, Bowser's Dark Matter Plant, Bowser Jr's Lava Reactor, and Bowser's Galaxy Reactor, while Super Mario Galaxy 2 has Bowser Jr's Fiery Flotilla, Bowser's Lava Lair, Bowser Jr's Fearsome Fleet, Bowser's Gravity Gauntlet, Bowser Jr's Boom Bunker, and Bowser's Galaxy Generator.
- Makron's hollowed out asteroid at the end of Quake II.
- Vohaul's asteroid base in Space Quest II: Vohaul's Revenge.
- The Third Moon in Strider.
- The Karma Fortress from Asura's Wrath.
- From the Mass Effect series, Kronos Station, home to the Illusive Man. Seen in cutscenes in Mass Effect 2 and visited during an Alliance raid in Mass Effect 3.
- In Planetary Annihilation, it's possible to send construction units up to moons to set up your own moonbases. Among the things you can build there are engines, for when you don't want the moonbase any more.
- In Something Else, the evil guy's true base is located on the moon.
- In Command & Conquer: Red Alert 2: Yuri's Revenge, the renegade Mad Scientist Yuri singlehandedly develops spaceflight so he can built a fortified base on the moon. He plans to retreat to his moon hideout after the Psychic Dominator network has mind controlled the planet. You'd think he might want to rule over his world of slaves instead of invading space, but he is a cartoonish supervillain.
- Mastermind World Conqueror has this as an option (alongside an underwater base, a skyscraper, a haunted castle...). It's easily the best in the game, since the lack of oxygen prevents vehicles from being deployed, leaving only infantry to attack. And wouldn't you know it, flamethrowers are very effective against infantry but not vehicles...