Ah, the Heroes R Us HQ. For some heroes, it's the place they eat, sleep, and generally live their lives; for others, it's a great place to kick back, relax, and have wacky hijinks with their friends while on downtime; and for everyone, it's the perfect place to run to after a failed mission, or at least an especially difficult one. After all, you gotta have a place for your heroes' R&R, and what better place than your very safe and secure Home Base, right?
Cue explosions, warning klaxons, and many "This Is Not a Drill" announcements. Somebody Set Up Us the Bomb indeed.
For shows featuring a Super Heroteam, a military group, a secret service, or anything else that requires a Mission Control to operate, an attack on their headquarters is a great way to increase drama and tension. When an ordinary mission is botched, the heroes still have some place to return, lick their wounds, and plan their next encounter; but if they lose their homebase? Big morale crusher right there. Not only have they lost a safe haven and one of their biggest resources, but for many heroes, their very home as well.
If it gets destroyed while the heroes are out (or worse, despite their best efforts), have fun Watching Troy Burn.
This situation is when The Mole frequently surfaces. You can also expect the story's Supporting Characters to have their own (freaking AWESOME) moments, typically tied into their position - the agency's weapons guy will break out the big gun, the university physics professor will cobble together a death ray while the math teacher calculates firing solutions, the magical gardener will animate the topiary animals, etc.
Naturally, this is a great excuse to Trash the Set. If the attack succeeds and the base falls, it could create a Shocking Defeat Legacy. Compare with Die Hard on an X, where at least one character is left to fight back after the initial attack, win or lose. See also The Siege, Protect This House. When the heroes pull this on the villain, it's Storming the Castle. If the destruction is upgraded to the entire city or country, this may be a Throwaway Country.
Often occurs at the beginning of videogames where you must fight Back from the Brink.
If you are looking for a trope related to the phrase "All Your Base Are Belong To Us", see Zero Wing. Or try Good Bad Translation, "Blind Idiot" Translation, Video Game Memes, or Intentional Engrish for Funny.
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Happens rather often in the Mazinger saga, since several of the plans by the Big Bad involve attacking the Photoatomic Institute. The Photoatomic Research Institute from Mazinger Z, the Fortress of Science of Great Mazinger and the Space Science Lab from UFO Robo Grendizer are preffered attack targets and often they get severely damaged, specially the first one. The worst damage the Institute suffered happened in the episode 34 from Mazinger Z, when Genocyder F9 turned the place into smoking ruins. Great Mazinger's HQ was not destroyed in the anime, but in one of the manga versions it was completely obliterated. The heroes were driven out of it and were forced to run away and lie low for a while.
Mazinkaiser also features at least four attacks on the Institute, which is finally destroyed in the General of Darkness movie.
Happens in Full Metal Panic!'s first season, during the last episodes when the villain takes full conrol of the Tuatha de Danaan.
In the yet unadapted novel Tsuzuku On My Own most (presumable, all) Mythril bases get thoroughly trashed by Amalgam forces with their biggest and meanest armslaves. Lots of people were killed and Danaan crew had to evacuate the Merida base in a hurry, without completing repairs and resupply of their sub. With Sosuke off-site, once again trying to save Kaname from kidnapping attempts and, now, Leo's advances. He fails. Unsurprisingly, the book ends on the biggest cliffhanger in the series.
The Hanagumi lose their theater (which contains their secret base) in this manner near the end of the 26-episode Sakura Taisen anime.
Also happens during the second season of Mobile Suit Gundam 00. As Celestial Being is getting resupplied at an asteroid base, Manchurian Agent Anew Returner exposes the base's location to the A-LAWS, resulting in the entire place getting blown up.
Happens in the Super Robot Wars Original GenerationOVA (later gets carried over to OG Gaiden). An exhibition of new mecha series...nothing could go wrong with that. Except that those new mecha series got their AIs rigged on their own and goes berserk without warning. And the result was lots of casualties, the heroes too late to prevent that, and five of the main characters captured. OG Gaiden adds up with the sudden kidnapping of one civilian in the middle of chaos. Getting their base attacked happens at least once per game throughout the entire series, if for no other reason than the fact that it happens so darn much in other anime series' (such as the ones included in those games).
A late episode of Yes! Pretty Cure 5 featured NutsHouse, the store that serves as Pretty Cure's headquarters (and Coco, Nuts, and Milk's home), being turned into a Kowainaa.
Late in Tokyo Mew Mew, Quiche kidnaps Ichigo and torments her with a vision of his fellow Quirky Miniboss Squad members attacking her friends at Cafe Mew Mew. After Ao no Kishi bails her out and they run back to base, it turns out to be true.
Midway through Mai-Otome, Garderobe is preparing to graduate/promote its new Otomes, and at the same time celebrate the grand re-opening of Mashiro's newly-reconstructed castle. Of course, they weren't counting on Schwarz spies being involved in the reconstruction effort, or on the castle being converted into a Slave-summoning superweapon. Things go rapidly downhill from there as Nagi assumes control of Garderobe, and Mashiro is run out of town.
And let's not forget the time Iruel pretty much took over Nerv's computer system and set the base to self-destruct before Ritsuko stops it with the single, free, uninfected MAGI system.
EI-15 in GaoGaiGar was produced from a programmer who didn't get picked to operate the heroes' base. As a Zonder, he infected the base computer itself, taking over all the systems. It took a double Big Damn Heroes moment by Volfogg infiltrating from outside while Entouji, the actual GGG programmer, trying to retake the system from the computer end. On its way out, the Zonder assimilated several spare GaoGaiGar parts, including some that let it mimic and counter GaoGaiGar's moves. Whoops.
And then there's the time seven of the Primevals infiltrated the GGG's Orbit Base through a 0.02mm hole in their force field...
Voltron: The Castle of Lions comes under attack multiple times in the course of the several series.
Happens in Hellsing when the Valentine brothers, Jan and Luke, attack Hellsing HQ with their squad of ghouls. They kill most of the mooks, but Alucard and Walter dispatch them quite easily. It is then found out that they were members of an army of Nazi vampires who are planning to start World War 3 for fun. And further down the line, it's revealed that Walter was the one who tipped them off.
Happens again with Zorin leading an attack on HQ when the Nazis arrive in London. This attack was far more successful, leaving the headquarters in ruins and bringing the Hellsing organization down to three members before being defeated.
In Gatchaman, Galactor finally manages to destroy the heroes' base in episodes 91 and 92. The American Battle of the Planets never reached these episodes.
Yes, it did. The two-part "Invasion of Space Center" was a revamp of those episodes. However, since the show had added 7-Zark-7, they had to explain why the robot wasn't destroyed or even threatened by separating Center Neptune into two parts: Space Center and Research Center.
In Ghost in the Shell: Stand Alone Complex, corrupt government officials order the attack on Section 9 headquarters by using Umibozu commandos. Being warned of the attack in advance, the Major prepares for a fake defense and blows up most of the facilities to hide their escape.
The original Getter Robo series had the lab destroyed by the Dinosaur Empire just before the final episode.
The Orochimaru/Sunagakure attack on Konohagakure during the Chunin Exams arc. After fending off these enemies, the residents of Konohagakure simply rebuild.
Pain's attack on Konohagakure in which he uses his jutsu to wipe the village off the face of the planet. Due to a Deus ex Machina, no one (except Tsunade) is seriously injured and...they simply rebuild again.
In Part 3 of the five-part finale of the Kirby anime, Dreamland, Kirby's home country, gets attacked by fleets of Destrayer ships sent by Emperor Nightmare and his company, Holy Nightmare Co./Nightmare Enterprises.
Both Gravion and Godannar had episodes where a piece of a destroyed Robeast hitched a ride on the heroes' mecha and started to grow and/or multiply inside their base.
In one of the rare moments in Transformers Armada where he wasn't holding the Idiot Ball or having the Autobots' newest gimmick ruin his plans, Thrust managed to draw the Autobots out to the battlefield, see that none of them had the Requiem Blaster, and then invade the now-unguarded Autobot base to steal the blaster while leaving Starscream as sacrificial decoy. It worked, but Starscream wasn't happy about it.
Fairy Tail's guild build can't seem to last 2 arcs without getting wrecked or other wise lost. To date, it was wrecked during the night by Gajeel and later totally demoloished during the fighting of the Phantom Lord arc which was the 2nd arc, the rebuilt version was warped into Edolas two arcs later though later restored, and almost immediately afterwards the key members leave for a mission and the building is repossessed while they were away as the weaker members left behind couldn't keep the guild out of debt. It remains to be seen if they will ever get the old building back.
Interesting subversion of this in Kurt Busiek's Astro City, during the "Tarnished Angel" story arc. The protagonist, a minor-league supervillain trying to go straight, has to stage an attack on the Honor Guard's floating home base. (Honor Guard is the AC version of the JLA). He's not trying to blow it up, though — he just wants to get the Honor Guard's attention and this is the only way he can think of to do it. So he blows his way in and then just stands there while the heroes come charging up to defend their home base. (Naturally they are not pleased with his method of getting their attention and they fail to listen to his story or help him the way he'd hoped.)
The Xavier Institute of the X-Men has been attacked — and destroyed — often enough that it's the subject of occasional Lampshade Hanging and in-jokes within the comics.
So often in fact that it's been outright abandoned at least twice. This just leads to their San Francisco island/Outback village/giant downtown spaceship/mystic lighthouse getting trashed instead.
Played with at the end of Batman: Dark Victory when the villains manage to invade the Batcave. However, the villains find it entirely by accident (they're simply trying to escape the chaos in the sewers) and are completely unable to capitalize on their find before Batman and a debuting Robin take them down. Most of the villains probably aren't even aware where they actually are.
Used for ironic purposes in Batman: Cataclysm. Every Waynetech building survived the titular giant earthquake because Bruce Wayne made sure all his building were quake-proofed. Unfortunately, the Batcave and Wayne Manor were not.
In addition to the X-Men mansion, the HQ of the Fantastic Four gets blown up real good on a pretty regular basis (and invaded from the Negative Zone and other fun stuff). It's a downside of not having a secret identity and having your base be a well-known landmark and tourist destination. They usually rebuild it quickly with improvements, but sometimes there are lasting effects: during John Byrne's run on the book, he had Annihilus attack and trash the place while Alicia and Franklin were at home. Franklin's New Powers as the Plot Demands failed to activate and both of them wound up seriously hurt in the hospital for weeks. The FF were very much not happy.
Recently, Reed has gotten Genre Savvy about this and designed the Baxter Building to be able to rebuilt itself after an attack.
He has actually tried that in his second appearance in comics. A Doom imposter later succeeded.
Captain America wasn't pleased either in the aftermath of the Avengers storyline "Under Siege", where supervillain Baron Zemo and the Masters of Evil succeed in taking over the team's headquarters.
Considering the fact that the Masters not only injured fellow Avenger Hercules, as well as faithful butler Jarvis, but Zemo tried (in vain) to break Cap's spirit by destroying his personal effects, which included the only photo of his deceased mother Sarah, as well as his original triangular-shaped shield, his reaction is probably justified.
As a result of this attack, the Avengers ended up moving their base to an artificial island named, naturally, Avengers Island. The fact it's mentioned on this page can probably tell you what happened to it.
Doctor Strange's Sanctum Sanctorum is similarly imperiled on a regular basis (once while it was serving as the headquarters of the New Avengers). He always comes back to it.
The Second Titans Tower, home base of the Teen Titans, was designed to address this problem with the whole above ground building being a hologram to attract enemies intending mayhem.
A defining moment in the original Teenage Mutant Ninja Turtles comic book: after Baxter Stockman unleashes his Mouser robots, they destroy the turtles' lair, forcing the turtles to relocate to April's apartment. Afterwards, the Foot attack the apartment, setting it on fire and forcing the turtles to relocate to Casey's grandmother's farmhouse in Massachusetts. Said story was eventually adapted in the first movie and second cartoon, with minor changes: in the movie, the Foot are responsible for both attacks, and in the cartoon, the turtles are present for the initial attack (only Splinter is present in the original).
Occurs twice in Sonic the Hedgehog, the first when Robotnik learns the location of Knothole and attacks it in the EndGame arc, and the second when Dr. Eggman decides to say "screw it" to his stalemate with the Kingdom of Acorn and rains Death from Above with his Egg Fleet burning it to cinders.
Tends to happen a lot with Flynn's run. The Evil Twins of "Moebus" managed to take Freedom HQ (which is all that's left of Knothole from said Death from Above) but this time, they could crash at New Mobotropolis (they got it back). However, with the Iron Dominion figuring out that they could control the helpful AI there, let's just say they press their advantage and take over the city. This time, only a few manage to get out but several of the heroes manage to fight within the city.
Then Eggman launches an attack with the Death Egg Mrk. II, which is temporarily interrupted by the Cosmic Retcon of the Genesis arc, and resumes once the retcon is undone. This includes releasing the Titan Metal Sonic to wreck havoc. Oh, and this all coincides with an Evil Plan by Ixis Naugus to usurp control of the city. The former fails; the latter doesn't.
And just when they're recovering from this, the Battle Bird Armada attacks the city and destroys the royal palace.
Eggman launched another attack on the city, but was repelled by the efforts of Team Freedom (with some anonymous aid from the Secret Freedom Fighters) and the fact that the Death Egg was running low on power.
This has happened to the Justice League satellite a number of times. At one point, the writers had to promise to not destroy it anymore unless they rebuilt it first.
In H'el on Earth, H'el throws Superman and Superboy out of the Fortress of Solitude to use the technology in it for his plans. The fortress is so impenetrable that Superman has to call up the Justice League to launch an attack on it.
Not related to Equestria, but this happens in My Little Pony: Friendship Is Magic (IDW) to the uber cute kingdom of cat people that Chrysalis and the Changelings land in after getting blown across the sky in A Canterlot Wedding. They promptly twist the place into their own image and drain the populace of their love, indicating that the Changeling Kingdom we've seen in the comic isn't the original. By the time the Mane 6 have gotten to the Queen at the start of issue #4, all that's left are green-goop-covered homes and solitary heart-shaped greetings on the ground.
In Dungeon Keeper Ami, Alphel breifly takes over Mercury's dungeon in a joint strike with Keepers Arachne and Nero, while Nero creates a distraction forceing all of Mercury's minions to fight on a battle field of his choice. The battle is vicious and protracted; but in the end all three are defeated for an epic Crowning Moment of Awesome.
In Harry Potter and the Methods of Rationality to show how serious things are getting as the fic gets darker in Taboo Tradeoffs an as-of-yet unspecified person, but most likely Voldemort/Quirell, False-Memory Charms Draco and Hermione so that they both think Hermione tried to kill Draco and casts the Blood Freezing Charm on Draco to frame Hermione, all inside Hogwarts, the fortress of Dumbledore, Leader of the Light.
Drago later breaks into Section 13 (apparently through the air vents, which he calls a cliche) in an attempt to steal the Talismans. Fortunately, Karasu also breaks in, and keeps him distracted long enough for the heroes to show up and scare him off.
In Ace Combat: The Equestrian War, the griffins attack and besiege Canterlot from chapter 14 until 17. Earlier, in chapter 8, they take over Cloudsdale. It remains theirs until it's recaptured in chapter 14.
Night Of The Shy: Nightmare Shy begins her war against Equestria by attacking Ponyville in an attempt to kill the rest of the Mane Cast. She succeeds with Rainbow Dash and the Princesses. After the girls and their allies are forced to flee, Nightmare kills most of the town's citizens and burns the town to the ground.
In chapter 6, Nightmare's Diamond Dog armies, aided by a swarm of parasprites, lays siege to Canterlot. They ultimately succeed in killing a majority of the Royal Guard and overrunning the city.
The following chapter, she sends a swarm of cockatrices to attack Cloudsdale which quickly curbstomps the Royal Guard contingent there.
Burning Black: Remy attempts to destroy the Ivory Tower shortly after it's been built by hiring demolition teams, but is foiled when Timmy wishes a memorial of himself onto the building, placing it under the city's protection. Later, Remy attacks it himself brazenly with a tank and does serious damage to the tower before the tank is destroyed and he's run off.
My Little Castlevania: Due to the Castle dimensionally displacing the royal castle and everyone in it (including the Princesses) and replacing it, it's child's play for Dracula's forces to occupy Canterlot and wipe out the Royal Guard.
A New Hope features a straight example and inversion simultaneously, with the Death Star coming after the base on Yavin IV and the Rebels attacking to stop it. In the EU the Imperial counterattack stretched out into a months-long siege during which the Rebels evacuated in stages.
The famous battle of Hoth in The Empire Strikes Back, one of the last permanent bases that the Rebel Alliance had before the Empire discovered it, necessitating a complete evacuation.
In Serenity, Mal discovers that the Operative has killed everyone who ever sheltered his crew in the past, including Shepherd Book.
Variation: In the live-action Ben 10 movie, the scene in which their mobile home is blown up by Eon.
Typically the enemy mooks burst into the heroes base and attack the Red Shirts, slaughter ensues, but all (or most) of the named characters escape to fight another day thanks to the heroic sacrifice of countless Red Shirts. Seen in Total Recall (1990), They Live!, and Logans Run.
Blade had this...and killed (indirectly) a main character no less!
The feat was zig-zagged in Blade II: the invading vamps wanted to recruit Blade's help. But played straight in Blade: Trinity, also with the death of a supporting character... twice! The Blade series really likes this trope.
Pirates of the Caribbean: Captain Jack Sparrow spends half his time getting back or stopping people from stealing his beloved ship, the Black Pearl.
In X-Men: First Class, the group move into the mansion in the first place when their previous HQ, a CIA compound, is attacked and destroyed by the Hellfire Club.
The opening of the 1995 Ian McKellen version of Richard III begins with a commando attack on the King's headquarters led by Richard of Gloucester, prefaced by an anachronistic Soviet tank crashing through the wall.
Batman Begins. Ra's al Ghul and his men walk right into the manor as guests at Bruce's birthday party. When he realizes who they are, he's quick to get everyone else out. Good thing, too, as they burn the house down immediately after.
The Dark Knight. The Joker and his henchmen invade Bruce's penthouse in an attempt to kill Harvey Dent. However, they never find out Bruce's identity as Batman, nor do they ever manage to get to Bruce's weaponry.
The Dark Knight Rises. Bane and his men destroy Wayne Enterprises R&D, and steals all the available Tumblers.
In the film Battle of Britain, based on actual events, the British air forces have a HQ which controls all fighter squadrons that gets hit and almost destroyed.
The Last Starfighter the Starfighter base is destroyed by an attack killing all the Starfighters except Alex, who had returned to Earth
In Get Smart CONTROL headquarters is attacked by KAOS.
Happens in Independence Day, the aliens take out every major military base in the second day of their invasion, including NATO's headquarters, the president then assumes command and control in Area51, which is a safe haven because of its top secret nature.
In Iron Man 3 The Mandarin launches a missile attack on Tony in the hero's Malibu home.
In Star Trek: Into Darkness John Harrison targets several Starfleet installations on Earth, from a data storage facility in London to Starfleet Headquarters in San Francisco.
Harrison: Have I got your attention now?
In The Matrix, a large deserted apartment building used by Morpheus and team as an operations center is assaulted by Agents and their mooks after one crew member does a Face-Heel Turn in trying to return to the pleasant illusions of the Matrix in exchange for his information.
All of House Atreides base were belong to House Harkonnen in Frank Herbert's sci-fi novel Dune, with the Harkonnens using The Mole and other treachery to open a gap in the base's defense and attack under cover of night, with imperial troops on loan.
During the Trauma Conga Line that was The Dresden Files book Changes, this happens twice. First his office building is revealed to have been bought by Red Court vampires years ago, who have inserted explosives into the walls (and put up the rent) and proceed to blow it up. Then they firebomb his home. Also, he's seriously injured rescuing his neighbors.
Happens twice in the Percy Jackson and the Olympians. Firstly, in Battle of the Labyrinth, Kronus' army invades Camp Half-Blood via the Labyrinth, causing the titular battle. Secondly, in The Last Olympian, the final battle with Kronos takes place in the throne room of Olympus itself.
The Halo novels use the code "blood arrow" to indicate that all friendly positions on a planet have been overrun.
In Shakespeare's Henry V, the English come back to their base after kicking French butt at Agincourt to discover that some French knights had slipped out of the battle and killed all of the guards (small boys, mostly) left to watch over the baggage train. Hal gets royally ticked off: "I was not angry since I came to France!" (Based on a True Story)
It happens in the very first book, Into the Wild, when ShadowClan launches a surprise attack on the ThunderClan camp. Fortunately, ShadowClan is driven off.
Happens in Twilight, only it's the heroes doing it. Not wanting badgers that could threaten them on their new territory, the cats of ThunderClan drive a mother badger and her young out of their home. This backfires massively when a huge army of badgers show up in the climax for a Roaring Rampage of Revenge.
In Dawn of the Clans, the Followers of the Sun Trail are attacked in their camp on the moor by some foxes that want it as their new home. Gray Wing gets to show off his skills as The Strategist by getting everyone together and driving them off.
Happened to Sherlock Holmes, somewhat famously, in the classic Doyle story "The Adventure of the Empty House". Shortly after Holmes reveals that he survived his confrontation with Professor Moriarty three years previous, Moriarty's surviving right-hand man Colonel Sebastian Moran (a feared marksman and big game hunter) manages to track Holmes down to his Baker Street apartment, and comes dangerously close to assassinating him. Luckily, Holmes sets up a decoy dummy and flees Baker Street at just the right moment.
At the end of Power Rangers Turbo, Divatox and her Piranhatrons launched an all-out assault upon the Power Chamber and ended up destroying it, but got recalled by Dark Specter, who had captured Zordon, before she could take over the planet, prompting the Rangers to pursue her into space and kick off Power Rangers in Space.
After that, "villains attacking the base" became a staple of the Grand Finale. Lightspeed Rescue, Time Force, Ninja Storm, and Dino Thunder all include scenes of the Rangers' base (and, in some cases, home) being spectacularly destroyed. Lost Galaxy played with the format by having the heroes purposefully self destruct their spaceship base to deter their enemies.
Interestingly, in Dino Thunder, this trope got pulled on them because they were busy Storming the Castle. And by a character who, at that point, was no longer loyal to the Big Bad.
The series in which the Rangers' base is invaded but survives, we must add in Lost Galaxy (ship destroyed as well as most of station, but city dome of station gets relatively gentle landing), Wild Force, SPD, Mystic Force, and Operation Overdrive. That leaves Space, the ship did get invaded once during Space, just not in the finale.
Inverted in Jungle Fury: Casey gate-crashed the villain's hideout, beat the Big Bad out of his host body and then dragged said host body out. The Ranger's base, situated in a Pizza Parlor, is left untouched.
One of the cooler episodes of The Sentinel involved the Cascade police station being taken over and held hostage.
Every incarnation of Star Trek has done this with the various Cool Starships. Otherwise the various away teams would have been safe as soon as they could take a transporter out. Of course, this meant that they had the worst transporter room security ever.
One Original Series episode had an escaped prisoner (who turned out to be something else entirely) hiding in a crate of medical supplies, and making it all the way to the bridge without getting caught. It's a good thing the mentally unstable prisoner hadn't decided to shoot Kirk with his phaser.
Also, Khan took over the ship in "Space Seed", and the Kelvans took it over in "By Any Other Name".
One season of Deep Space Nine had the station being occupied by the Dominion. Gul Dukat seemed happy to get his office back, though, since from where the Cardassians sit (or at least Gul Dukat sits), the Federation pulled an All Your Base on them.
Also, this trope was inverted in a third season episode of Deep Space Nine. Sisko, Jake, and O'Brien accidentally set off a Cardassian counterinsurgent program which was "inadvertently" left in the station computer. This set off an increasingly ridiculous chain of hopeless death traps, with each successive death trap growing increasingly more fatal and overengineered each time the crew attempted to defeat the previous death trap. The kicker was when Dukat himself couldn't even disable the program.
The Borg pulled a "All Your Captain Are Belong To Us" by assimilating Picard, then shortly having the Borgified Picard send a message that "You have no chance to resist; make your time" to the Enterprise.
...and they took over the Enterprise, or at least part of it, in First Contact.
More embarrassingly, a group of Ferengi pirates snagged control of the ship using secondhand Klingon war surplus in "Rascals".
You get the picture by now, but for thoroughness' sake: psychic aliens took over the title ship in Voyager in "Waking Moments", after a fashion: the entire crew was trapped in a dream version of the ship in which they had taken over. Only Chakotay and the Doctor remained in the real world.
The crew members under the control of the Lotus-Eater Machine tried to keep Seven and the Doctor from keeping them from flying straight down the monster's throat. They were still in control of the ship, but they were definitely Not Themselves.
The second season finale had the Kazon-Nistrim taking over the ship outright and stranding the crew on a nearby planet, leaving their only chance to take it back in the hands of Tom Paris, Lon Suder, and the Doctor.
The Doctor (can you tell he finds himself in a lot of Die Hard on an X situations when this happens? Being a Projected Man has its advantages) and another EMH had to take back a ship the Romulans had invaded.
And in Enterprise, we can't forget the numerous times the Suliban have been able to get in and out right under their noses. They're a slippery bunch indeed. They also had to deal with the Borg once.
And the Ferengi.
A regular occurrence on Stargate SG-1, to the point where it is subverted in a later season: the final test for prospective team members is a simulated Die Hard scenario, complete with alien infiltrators and noble (yet harmless) sacrifices. In contrast with most other examples however, Stargate Command is designed and operated with the expectation that hostile forces would frequently attempt to invade, up to including a Self-Destruct Mechanism into the base design from the get go.
And in Children of Earth, the base (along with Jack) is completely blown up. Jack does better in the long run.
Also in Children of Earth: the government has Thames House, a super-secure building designed to withstand all sorts of attacks by closing down completely. Cool, eh? Except if you invite the enemy in, and they proceed to use these very characteristics to kill everyone in the building, just to make a point.
In "End of Days", as part of a plan to release a giant demon, Bilis infiltrates the base's holding cells to kill Rhys.
Doctor Who: This was one of Patrick Troughton's favored settings. When Jon Pertwee was stranded on Earth, his benefactors at UNIT became harried by alien visitors, too. It later went out of style until the reboot.
The 1996 movie shows the TARDIS being taken over by The Master and his accomplice. In the New Who episode "The Sound of Drums", the Master takes over the TARDIS, then subsequently the flying UNIT headquarters and the entire planet.
The entire Earth has been conquered on more than one occasion, especially in later seasons. The Daleks, Cybermen and The Master have all pulled it off, with different levels of success, with The Master arguably coming out on top.
In season 7 of Buffy the Vampire Slayer, Buffy's home becomes a literal base for their Super Hero team, complete a The Mole (The First, impersonating one of the Potentials), multiple sieges and examples of set trashing, until the end of the season, which climaxes with the ultimate Trash the Set.
This is also what Adam did to The Initiative in season 4.
Played with using the Watchers' Council—-their headquarters are attacked right as Quentin Travers is announcing their plans to go to Sunnydale and help Buffy fight the First.
For the first three seasons, the school library was where they always went to research, train, and plan for the upcoming confrontation with evil. Being (1) public space, and (2) the location of the Hellmouth, bad guys came there looking for a fight pretty frequently.
Got one of the more low-key, if still very creepy, uses of this trope in the third season finale. The Main Characters are all gathered in the library, discussing how they should bring down the Mayor (the latest Big Bad), when, Speak of the Devil, he comes in through the front door, not to attack them or interrupt their plans in anyway, just to see how they're doing and deliver a few threats while he's in the neighborhood.
Hard not to spoiler this simply by writing the show, but in Angelthe Angel Investigations building is blown up at the end of Season 1, to be replaced by the Hyperion Hotel starting in Season 2.
Inverted in the final season of Angel, it's more a case of "All Our Base Are Belong to You" — the Angel scooby gang ends up being given the LA branch of Wolfram and Hart to do with as they please.
And one episode plays it straight, with Wolfram and Hart being invaded by cyborgs.
Lampshaded late in Season 5.
Angel: Call security, put 'em on red alert. Nobody gets in this building without clearance from me. I want a guard at every entrance, every elevator, every stairwell. Cover the whole building.
Harmony:(shrugs) OK, but you know how that never works?
Harmony: On it.
Modified in the new Battlestar Galactica, mainly the miniseries: the Cylons don't exactly occupy battlestars. Rather, they take over control of them through the computer networks.
Season 2 begins with a Cylon boarding party attempting to take over the Galactica, and in season 4, Gaeta's mutiny succeeds in doing just that, giving Adama and Tigh a Die HardIN SPACE! opportunity
Played straight with New Caprica, where it's all your planet are belong to us.
Multiple examples on 24: During the course of eight seasons, attacks on the CTU included: detonation of a bomb, release of a canister of chemical weapon into the ventilation system, assault by a mercenary squad and activation of an EMP weapon. And these were just direct attacks, other minor hindrances to the protagonist consisted of computer viruses, various power plays and internal investigations.
Hell, it's so common it became one of the main plot points in the canon video game, which saw several missions devoted to CTU being taken over the antagonists.
Due too CTU being decommissioned at the time, season seven saw this happen to the White House instead.
The Goodies both played this trope straight and parodied it: they had a recurring base which featured almost any room you pleased behind the same two doors (thanks to Chroma Key), a window that turns into a video screen when you pull down the blinds, a huge 1970s computer, and so forth. Graham's Gadgeteer Genius status meant that they also had similar bases on ships or planes in certain episodes.
In one episode in season one of Alias, SD-6 headquarters is taken over by a team of baddies led by a guest starring Quentin Tarantino.
Also in season 5. APO HQ is bombed by The Mole/Magnificent Bastard, Sloane.
This happens too often in NCIS, whose base of operations is the Navy Yard, DC. You have to wonder how trained badass terrorists like Ari have to go to such trouble to infiltrate the place when any serial killer or stalker can just walk in bold as they please. Possibly lampshaded in one installment when Gibbs wants to shut the base down due to a serial killer's threat:
Vance: "Gibbs, I don't know if you've noticed but we run the navy out of the navy yard."
At the end of Episode 11 of Season 4 of Dexter, the Trinity Killer casually walks into Miami Metro Homicide, peruses the evidence being collected to catch him with bemused glee, and confronts Dexter in his lab, learning his real name and violating a space Dexter considered safe.
On a smaller scale than is usual for this trope, Dexter pulls this most episodes with his victim of the week: Taking control of a place they had felt secure, sometimes only symbolically by putting up tokens of their criminal life and asserting dominance, other times literally taking control of their home base (a scrap yard, a cabin in the everglades, a shrink's office, etc.)
In Flashpoint, an old sergeant of the team came by to visit. Only to take someone hostage when things didn't go like he planned.
Babylon 5, due to its nature, is threatened in one way or another almost every episode. However, there are at lest three examples of large-scale invasions by boarding parties.
In "Babylon Squared", Sinclair experiences a flash forward of the Shadows invading B5 if Sinclair had stayed on B5 instead of becoming the Minbari Ambassador).
In "Severed Dreams", Earthforce likewise boards the station in what becomes a very bloody struggle between them and station security.
"A View From The Gallery", which follows two random maintenance personnel as they go about their jobs...in the middle of a battle where aliens board the ship.
Attempted in Firefly, "Objects in Space", where Jubal Early successfully boards Serenity, knocks out and/or locks most of the crew in their quarters, and holds Simon at gunpoint throughout his complete search of the ship. Unfortunately for him, the ship fights back, when River pulls the same stunt on him.
Done twice in Merlin, when Morgana takes over the castle of Camelot.
Kamen Rider Dragon Knight - Tired of being subtle, Wrath and Strike go to the bookstore, hold Lacey and Trent hostage, and then tear the place to pieces in a knock down, drag out fight with Len and Kase. (Technically, the bookstore isn't an offical base but it is treated as one by the four good Kamen Riders (Len, Kase, Kit and Chris)
also suffered minor damage when Kit, Len and Chris nearly fought with Axe and Spear in the bookstore in an earlier episode, but at the end of the series, it was replaced by a better and bigger bookstore.
It is also inverted with 'Storming the Castle' at the end of the season, when the Kamen Riders storm Xaviax's mechanical fortress. (though the only thing they really destroy is the shield generator and Xaviax)
Kit's apartment, which serves as a 'base' for the Kamen Riders as well, remains intact.
Implied to have happened to the Kamen Rider Base on Ventara, Kase says in Swan Song that the survive mode cards were the last thing she grabbed before Xaviax destroyed their base.
Kamen Rider Blade: Happens at the start of the series -after a moderately successful mission and going home for the day Blade returns later that night to find the secret hidden base trashed and most of the staff dead-aside from the bridge bunny who gave him directions-after wards the take what hardware they can and set up shop in a country side cottage outside town. Managing to salvage the monster detector so blade can still fight monsters. Also even though the base gets wiped out the group board still seem to be sending him his pay check as later in the series he is shocked they stop-obviously pay roll and human resources were not at the base.
The Walking Dead: In the season 3 episode "Home", the Governor launches an attack on the prison in retaliation for the protagonists' strike on Woodbury two episodes previous. The attack claims the life of Axel and results in attracting a herd of Walkers to the prison.
In the Season 3 finale, "Welcome To The Tombs", the Governor leads another attack on the prison, this time a full-scale strike with a whole militia. The heroes lure them into a trap (namely a tunnel full of Walkers), and then drive them off.
In the Season 4 mid-season finale, "Too Far Gone", the Governor attacks again with his new group (which happens to include a tank). By the time it's over and done with, the Governor and most of his group are dead, as is Herschel, the Prison is in ruins and overrun by Walkers, and the Prison group is scattered.
CSI NY had one,a drug lord had his guys storm the lab in 'Snow Day'' and in 'Today is Life',the precinct almost gets it,though the rioters never get in.
In "Stand", Walter Sykes activates the Warehouse's portal link to the old Regent refuge in order to infiltrate it and both steal the Colodi bracelet and kill Jane Lattimer. This fails, and he dies, but he has the backup plan of bringing an Artifact WMD to destroy the Warehouse (requiring a Reset Button the following season).
In "The Truth Hurts", Paracelsus allows himself to be captured as part of a Batman-Gambit to completely usurp Mrs. Frederic's position as Caretaker and seize control of the Warehouse. This leads to a horrifying scene of the team being chased out of the Warehouse by lightning strikes and collapsing shelves.
The name of this trope comes from the intro of Zero Wing, which begins with an organization (or person?) known as "CATS" taking over the bases of the player's organization and attacking the ship the player is stationed in.
The Base Defense in the X-COM series is one of the more harrowing missions there is, especially if you didn't properly design your base. Not only does failing or quitting that mission mean you've lost the base (and if that was your last one, the game as well), but you lose any facility that was heavily damaged in the firefight as well.
Don't forget that you're often fighting terror units, who, with the exception of the Muton and Floater ones, are fearsome opponents, and have a battleship load of supporting aliens. You would not believe how much psionics are used in some of those. And they have blaster bombs.
And, if it doesn't happen to be the base that houses your elite squaddies (or they are out on a mission at the time), you often have to fight with a cobbled together band of scrubs.
Just to add annoyance, game's 80 item limit can cause troubles: Instead of high-tech heavy plamse weapons your rookies might end with beginner rifles and pistols, if you haven't sold them. Ever tried to kill a muton armed with plasma using conventional weapons?
Half-Life 2 features this. No less than twenty minutes after the player reaches the well-equipped and well-hidden resistance base outside of City 17, the Combine fly in with their helicopters and start shelling the place with headcrab canisters. The base is lost, and the survivors relocate to the White Forest Base, where, incidentally, the same thing happens... only this time, Gordon Freeman isn't cut off from the fray. Guess who wins.
Quite a few resistance bases are attacked, and some destroyed, later on through the game.
Freelancer, it's safe to say, beats this trope to death, then reanimates its corpse as a zombie and does it again. Almost every friendly base, capital ship or space station Trent steps onto in the story mode is likely to come under heavy assault within minutes. And he visits a lot of them.
Partly subverted in Suikoden V. where letting the enemy succeed in invading your base without any resistance is the correct choice, as it's part of a Batman-Gambit by The Strategist to wipe them out with minimal losses.
Also played...mostly straight at the game's beginning, where, after one extended playable flashback and a few missions about the kingdom, the heroes return to Sol Falena's palace, only for it to be attacked by the Godwin family and their ninjas. A possible subversion occurs, however, in that not only did the heroes suspect something was coming and prepare for it (including by dosing themselves with antidotes before the feast because they knew full well there'd be sleeping drugs in the food), but actually looked like they were going to win against the attack. But then the Queen's mad with power moment got out of control, as she went from vaporising the attacking ninjas to reflexively vaporising her husband...Things just went more and more wrong from there.
While most games in the Mega Man Classic series end with the titular robot invading Dr. Wily's (or, in the case of the sequel, Sigma's) fortress to take him out, Mega Man X3 started with an attack on the Maverick Hunters Headquarters.
The video game adaptation of The World Is Not Enough has James Bond fighting terrorists that invaded the MI6 headquarters, even though this never happened in the movie (the HQ was attacked by a remote bomb, but of course you can't shoot that so that makes for bad gameplay).
Bizarrely they did do this in the next film but it was a VR simulation.
Perfect Dark features a level where once again, the enemy sneak-attacks the good guy HQ.
Happens in Freedom Fighters: by the middle of the campaign, your base is taken over, and you have to find another place where you can run La Resistance.
For what it's worth, the main plot of Freedom Fighters is that Russians pull a Sneak Attack Coup on New York City, and the actual game is you in a Die Hard Situation.
The first hour or so of Metroid Prime 3 consists of a Space Pirate attack on both the ship you're on, and the base on the planet you're orbiting.
Occurs in the Command & Conquer games several times, in which Kane hacks into the player's character communications to taunt him following an attack on the good guys. It's most apparent in the Tiberian Sun GDI intro, which is eerily similar to the intro of Zero Wing.
Can also literally happen in gameplay — watch out for those Engineers....
This occurs in one of the later Gamma Campaign missions of Warzone 2100. NEXUS, the Big Bad intruder virus created by disgruntled Mad Scientist Dr. Reed hacks into the Project's Synaptic Links(which were also developed by Reed) and begins taking control of the player's units and structures.
The second level of Halo 3 is a textbook example of this, and in true Bungie fashion you traverse the majority of the base three times. Still fun though.
In fact, the two examples of Halo 2 and Halo 3 are just smaller battles in the greater All Your Base Are Belong to Us battle for the Earth itself. Also, the "Pillar of Autumn" moment of Halo 1 had you running away from an earlier All Your Base Are Belong To Us moment on the planet Reach.
Also happens with Sword Base in Halo: Reach twice before the planet itself is glassed. And you do get to set up the bomb the second time.
Bungie's earlier Marathon series starts off with you aiding in the takeover of an alien ship during their invasion of your colony. The sequel has you performing a planetary invasion of your own from it until the ship is taken over by a hax0ring AI, and you instead flee to a makeshift planetary base camp.
...which is then belonged to walking bombs disguised as humans.
Star Trek: Elite Force and its sequel have levels like this, on the Voyager and Enterprise, repectively. In the second game, you even have to fight off enemies on the outside of the ship.
Mass Effect 2 had another variation: All Your Ship Are Belong To Us. Twice. And the first one completely destroyed the original Normandy, and the second almost completely wiped out the crew of the Normandy SR2.
The final outcome, depending on your last decision, is either All Your Collector Base Are Destroyed By Shepard, or All Your Collector Base Are Belong To Cerberus.
And now, to complete the trifecta, Mass Effect 3's trailer has All Your Earth Are Belong To The Reapers.
And later in the game All Your Citadel Are Belong To The Reapers. Again.
Neverwinter Nights 2 has an entire quest arc dedicated to such antics: should you choose to aid the City Watch, it falls to you and your compadres to expel sundry unsavory characters from the Docks district. If it were anything other than your own city it would be more like Storming the Castle.
And then there is the scene in between acts 1 and 2 where the Githyanki storm the Sunken Flagon and kidnap Shandra (again)
There's also the assault on Crossroad Keep.
Lunicus had you and your buddies striking out from the titular hidden moonbase to fight an alien occupation of earth. It gets invaded later in the game, allowing you to hijack one of their boarding craft to pull an Independence Day.
The last mission in Soldier of Fortune II: Double Helix takes place at the Shop HQ, which has been taken over by the main terrorist organization.
Irrational Games' Freedom Force features giant robots attempting to destroy the Freedom Fortress, and a successful invasion of Giant Ants.
For the first half of Silent Hill 4 your apartment is a haven where you can heal and rearm. In the second half of the game it is overrun by ghosts who can hurt you by proximity, and who will contribute to giving you a worse game ending if you don't clear them out.
Final Fantasy XI has Besieged, wherein the city of Al Zahbi is, from time to time, overrun by beastmen. There's also an infamous 3-month period where the cities in "Wings of The Goddess" were faced with constant invasions because the enemies in Campaign were so damn strong it was nearly impossbile to hold any areas so city invasions wouldn't happen. Additionally, in one scene during the Battle of Jeuno mission arc, the Allied Forces of Altana are presented with an ultimatum from the Beastmen Confederacy. The orc presenting the surrender treaty says outright "You press seal here. Then all your Jeuno are belong to us". After the player and other npc heros break up the meeting, that same orc yells "You have no chance to survive! Make your time!" One wonders what the game's japanese script had in the same scene.
In Final Fantasy VIII, enemy forces invade and conquer Irvine's home, Galbadia Garden, then use it to do the same to Balamb Garden. After many difficult battles in the halls of his own home, and successfully fending off the invaders, Squall leads his SeeD classmates to counterattack and retake Galbadia Garden.
In Final Fantasy IX, every city that is allied with or is home to the heroes is either conquered or downright annihilated by Queen Brahne of Alexandria.
In Knights of the Old Republic, the Ebon Hawk was inviolable to anything less than a full squadron of Sith fighters plus a poorly timed bathroom break/bikini-wearing spouse/cardiac arrest (or all three); the sequel, well...not only do you have to keep Sith troops out of it with a turret, but later, it suddenly fills up with pissed-off slavers for you to kill, and even intrusive Sith who can pull a Face-Heel Turn and even become a romantic interest, depending on how nice you are.
KOTOR 1, the Jedi Enclave on Dantooine is razed by Darth Malak's forces after you complete three planets.
In Starcraft, the Zerg can infect a Terran Command Center, seizing control of it, and use it to produce Infected Terran units.
Not to mention the big plot points where the Zerg take over, oh, let's see: Chau Sara (to start the game), Mar Sara, Tarsonis, Aiur, Char, Antiga (Nobody remembers Antiga...) Not to mention the Jacobs Installation (All Your Base's Secret Intel Is Belong To Us), the Amerigo (All Your Spaceship's More Secret Intel Is Belong To Kerrigan), and one incident in the novels where Raynor shipjacks General Duke himself, ending up with the Hyperion.
The eminently quotable Michael Liberty had this to say about this state of affairs:
Michael Liberty: We had the advantages of interior lines of supply (that's military for "surrounded") and native terrain (that's military for "we're fighting them in our living rooms").
And in the final level, Ratchet and Clank get their revenge by infiltrating Dr. Nefarious' base. All alone, though (although Captain Qwark shows up for a bit in the end).
Ace Combat 5 the neccesary-to-spoiler-tag scene where your new base is sunk by two sub-launched missiles. Before that, the first three levels of the game are the build-up to and execution of an attack on your first base. Later on, the bad guys (who weren't actually bad) also attempt a seaborne invasion.
Zero tops this with the XB-0, a Belkan superweapon attacking and disabling your base
Allowing the enemy to reach your starting stronghold in the Ogre Battle games is an instant Game Over.
Not so much in the March of the Black Queen - you lose the level and take a big reputation hit, but you can try again with no other consequences. The only Game Over condition is the death of the main character.
One of the final missions in Dungeon Keeper 2's campaign has an interesting version. You are set up against the goodly King's right-hand man Lord Pureheart and his map-spanning fortress with an overpowering number of guards and other heroes only a single alarm away from your Dungeon Heart. Your base is tucked in a very meager niche of diggable rock to prevent traditional means of building up power and your resources in general are limited. The correct strategy is to slowly and quietly block off (with the help of the just-unlocked Secret Door) and take over the castle, starting from the outlying torture dungeons and storerooms while picking off and converting the patrolling guardsmen to your side one at a time. Ideally, after the entire castle has been silently subverted, the siege ends with the former heroes launching a massive attack into the Lord's throne room at the very core of the castle. Surprise!
Red Faction: Guerrilla: In the middle of a missions the game pulls a swerve: without warning the mission is aborted and you have to race to save a safehouse from a full-on assault. The safehouse is wrecked and your commander is killed.
In Dead Rising, the zombies start to encroach on your safe zones, appearing in the warehouse and elevator in greater numbers as the game proceeds. Following the main plot missions will eventually lead to commandos taking over the mall and your original safe room. Though Frank inverts this by taking over the enemy's secret hiding place and hiding there for the remainder of the game.
Oni has this happen in its 6th chapter, just after losing Muro's trail in chapter 5.
In the endgame of Dragon Age: Origins, the Darkspawn attack Redcliffe and Denerim. You get to Redcliffe just in time to save the castle and everyone in it. Denerim isn't so lucky. By the time your forces get there, the Darkspawn have already established a foothold in the burning city and presumably killed everyone who couldn't escape in time.
In several of the Ys games, the game's main town gets occupied by the enemy and its residents captured.
Mechwarrior 4: Black Knight features a nasty one. While you're out on patrol after taking a big bite out of the enemy war machine, House Steiner betrays your mercenary outfit and launches a surprise attack on the base. In the ensuing chaos, Colonel Badass and Mission Control are both killed, many survivors are taken prisoner, and you pretty much only make it out of there with a few civilian trucks plus whatever gear your Humongous Mecha squad had equipped at the time.
Theoretically any mission in Mechwarrior 3 can become this if you position your Mobile Field Base too close to the bad guys.
Samurai Warriors: The first game in particular had castle sieges, parts of the game where you infiltrate the enemy stronghold and kill the enemy. This was not a popular gameplay mechanic and so the castles became part of the main war map itself, and depending on whose story battle you were following you had to either invade or repel an invasion on your home fortress. The most iconic of this is the siege of Honnoji, in which Mitsuhide Akechi turns against Oda Nobunaga,
In AdventureQuest Worlds, the main villain of its recent Skyguard storyline is a guy named Master, who plans to infiltrate the Skyguard to cause enough mayhem to make Drakath decide to make him the next Lord of Chaos. Shortly after the Skyguard induction ceremony ends, an attack is launched against the Skyguard Academy, and the academy is being invaded by Chaobolds, Bronze Sky Pirate Draconians, and an Inbunche waiting at the academy's cafeteria. And that's not all - Invidia, one of the Skyguard's newest recruits, could actually be The Dragon to Master, the Dreamweaver, in disguise. They do look familiar, after all...
The Reconstruction, towards the end. The world is devastated by floods and a volcanic eruption, then the Big Bad destroys what's left. As a result, Wadassia, the city where most of the cast hails from and the main base of their operations, is reduced to ruins, in addition to every other city on the planet. Since the main character is heavily devoted to Wadassia, this also causes him to have a major Freak Out.
Martian Elder: "A rapid offensive to (the humans') social and economic heart should prevent any significant opposition."
The Martians actually do this twice. The first time (a direct assault on London, shown during the intro movies) it backfires because they underestimate the humans' firepower. They then change their landing site to Scotland, which works much better - whichever side you play the campaign as, the Martians will be in control of most of Scotland by the end of the first week or two.
Twice at the beginning of Deus Ex: Invisible War. First the Tarsus base in Chicago gets destroyed by a Templar Grey Goo bomb, then the Seattle base comes under attack by the Order.
The first game started on Liberty Island, UNATCO headquarters, which was being occupied by NSF forces, although the actual base was not captured.
The third game started with the Sarif building being attacked by hostile mercenaries and supersoldiers.
The Game Of The Ages: You should have suspected this would happen as soon as you got a look at all the castle's defenses.
Happens towards the end of I Miss the Sunrise. The Inquiry, the spaceship that serves as the home base for your crew and as The Hub for gameplay purposes, is destroyed by the Big Bad in the final episode.
Seems to happen in New Super Mario Bros U, where instead of Peach getting taken to Bowser's Castle, Mario and co are flung out the castle and have to make their way back there.
Villages in Battle for Wesnoth. Trivial to take over when unoccupied, a pain to claim if held by a hostile unit (you need to get rid of the defender first, who'll probably enjoy a cover bonus and heal between turns while your attackers don't, and then still move a unit of your own in after that battle is finally over), and yet absolutely vital to each side's ability to recruit, support, and heal its units.
The second-to-last mission of the Operation Final Fury plot in X3: Terran Conflict has you called back to base with little ceremony. You enter the base's sector to see an enormous Kha'ak warfleet doing its level best to kill everything in sight, including the base.
Buck Bumble has the titular bee going out and destroying Herd satellite installations that would let the Herd find out where the Resistance base was. The very next mission is the base calling Buck back frantically, because the Herd found them anyway and overran it.
During the Waters of Life quest in Fallout 3, the Enclave storms the Jefferson Memorial and seizes Project Purity, jumpstarting the game's second act. Earlier, as the evil solution to the Tenpenny Tower sidequest, you can let the Ghouls into the building to massacre the residents. You can also arrange to have them move in, but they eventually backstab and slaughter the residents anyway. You and the Brotherhood also do this to the Enclave, twice if you have the Broken Steel DLC.
This happens to Wario himself in Wario Land II - neglect to wake up at the beginning of the game and the invading pirates throw you out the window and take over your castle, forcing you to reclaim it.
This happens in Star Fox 64 if the player takes a route through Sector Z. The Star Fox team's mothership, Great Fox, is attacked by a swarm of enemy fighters as well as several missiles.
Touhou: In Scarlet Weather Rhapsody, an incredibly weak and localized earthquake destroyed the Hakurei shrine, a building that not only is the main character's residence, but is also built upon the barrier that separates Gensokyo from the outside world (so it's actually very important). This makes the heroine going mad at it, and she goes out for the culprit, a celestial being named Tenshi Hinanawi that purposedly caused the incident because she was bored and wanted someone to fight with (and she gets kicked a lot by nearly any character in the game, excluding Remilia Scarlet because she couldn't go out due to the inevitable exposure to the Sunlight). Tenshi is eventually forced to rebuild the shrine, but Yukari Yakumo destroys it again because she noticed that Tenshi rebuilt it to please her own tastes. Then, the shrine is rebuilt a second time by Suika Ibuki, with the help of some Tengus.
The Order of the Stick: Most of the third arc is dedicated to the Order and the forces of Azure City defending the city from the hobgoblin/undead army led by Xykon and Redcloak and eventually being overrun.
Later in the comic (warning: spoilers!), Redcloak's forces have also managed to crush the resistance in Azure City, killing every member of the resistance except for Niu and destroying their mountain base.
Whateley Academy has had its (in)famous Halloween attack. No students actually died, but this was primarily due to most of them being incapacitated right from the start and the attackers being under orders not to actually kill any students except their assigned targets anyway; the campus security forces weren't as lucky.
In Protectors of the Plot Continuum the PPC's headquarters has been invaded repeatedly, though the 2006 attack and prelude to the 2008 invasion were the only ones that had any real success.
When Tarot attacked the sattelite base of the Global Guardians in force, it resulted in the near death of two Guardians, two civilian contractors who were onboard, broke the base into pieces, and knocked those pieces out of orbit. The parts of the base that didn't burn up on re-entry crashed into the Pacific and Indian Oceans.
The season 2 finale of We're Alive ends with the fall of the Tower.
The Gungan Council has Naboo being the headquarters of the Jedi. This makes it a frequent target for attack, with the most prolific one being the year-long "Theed Under Attack."
Happened a few times in the Justice League series. From the dream invasion by Dr. Destiny to the C.A.D.M.U.S. attack led by Galatea, the Supergirl clone.
They use the Batcave as a back up base and that was also raided at one point.
H.I.V.E. took over the Teen Titans' base in the third episode (but first episode aired) of the cartoon , and to say the least, it certainly wasn't the last time such an event took place. One notable occurrence was when Slade attempted to destroy the base, but it turned out to be a Batman-Gambit to have Terra earn the Titans' trust by saving it.
The most notable example is probably two episodes later "Betrayal" when Terra deactivates the security system to let 200 armed robots in undetected.
Befittingly, the Titans East's base would later be taken over in their debut episode.
Beast Wars had an episode where a Starscream-possessed Waspinator spearheaded the (temporary) takeover of the Maximal base.
Later, Rampage destroys it, by 'shoving it off a waterfall, forcing the Maximals to find a new base.
In Avatar The Last Airbender, the Fire Nation takes over the city of Ba Sing Se, effectively conquering the Earth Kingdom and forcing the heroes to go incognito after escaping the city.
Earlier in the series, Aang, Katara and Sokka arrive at the city of Omashu only to discover that it has fallen to the Fire Nation.
More true to the trope is the Siege of the North, when the Northern Water Tribe, secure for generations, was subjected to a massive assault when the Fire Nation learned Aang was there. Although in that case, they successfully defended themselves. Having a giant koi fish fight for them certainly helped.
Let's not forget "So The Drama", where Drakken took over the Bueno Nacho corporation...
And that in both the movie and the grand finale her house gets totalled.
Also occurred in Danny Phantom when the hero's Local Hangout were violently invaded by the Guys in White by order of Vlad who bought the franchise briefly to torment Danny.
A variation appears in proper English in the Static Shock episode "A League of Their Own" (part one). After Static blasts down the buzzsaw-handed cleaning robot, Brainiac says "You only delay the inevitable. All of this base will soon belong to me."
In Codename: Kids Next Door, Sector V suffers this a lot, as their treehouse is taken over/destroyed/stolen by their archenemies, The Delightful Children, turnips, Santa's Elfa Strike Team, and their own organization being manipulated by The Mole.
Happens several times on ReBoot, particularly since the heroes' headquarters doubled as the control post for the entire Mainframe.
Happens all the time on Code Lyoko. Not surprising considering the enemy's physical form is also the computer they use for their operations (at least until Season 3).
Aside from the adaptation of the comic book story referenced above, the second Teenage Mutant Ninja Turtles cartoon had this happen again, when Karai attacked the turtles' second lair, completely trashing it and forcing them to relocate to a third lair.
Happens in the Hunter's Moon arc of Gargoyles with the destruction of the Clock Tower by the Hunters.
Occurs in the first season finale of Generator Rex. Van Kleiss and his henchmen hijack the keep, and ram it into Providence Headquarters, then go to town on the place. Predictably, dozens of Red Shirts die in this episode.
In the DC Super Friends short, Joker takes over the Hall Of Justice with help from Gorilla Grodd and Mr. Freeze.
In the second season finale of Super Jail, The Ultraprison crew has taken over the titular jail while the main cast and other prisoners have been on their cruise and got lost for two months.
Transformers Prime: Near the end of the second season, Starscream uses the abilities granted by Red Energon to sneak into the Autobots' base through their GroundBridge and steal the Omega Keys. He would have done more (he states his desire to gut Arcee, for one), but he was on a time limit.
Topped big time three episodes later in the season finale. After creating a fortress on Earth within line of sight of the Autobot base, the Decepticons launch a full-scale assault, culminating in Megatron using the Nemesis' Wave Motion Gun to obliterate the entire mountain... with Optimus still inside.
Any number of real military forces have had this happen to them. Either because of surprise or defeats on the battlefield, the defenders find themselves fighting in their own front yard. At the end of the war, this may be combined with a Bolivian Army Ending for the losing side. Can also happen at the beginning of a war.
Doolittle Raid. Two U.S. carriers launched a small fleet of bombers that firebombed Tokyo in early 1942. Tactically, the raid was not too important as nothing important was damaged and over half the bombers were lost, but it did a fantastic job of boosting U.S. morale and lowering Japanese morale in the capital city, in addition to forcing the Japanese to hold back many of their forces to defend the Home Islands from further attacks.
Kind of the point actually. Firebombing Tokyo made the Japanese realize that their "Sacred" nation was vulnerable to attack, made them divert resources to protect space the allies had no real immidiate interest in and weakened them on other fronts, making them easier to defeat in battle.
Another (in)famous example is the Tet Offensive of 1968, where a massive sneak attack managed to breach the perimeter at some of the "safest" places in Vietnam.
And ended in the complete destruction of the Viet Cong as a cohesive fighting force. Although a surprise, and political turning point, the attack was not a military success.
But then, the war was not entirely a military war. The Tet Offensive is a case of a battle being a Tactical defeat and a Strategic victory.
Second Ypres - the Germans almost, almost got through the British defenses with the help of poison gas. It came down to second-line troops attacking German Guards regiments, convincing the Germans that the British were still strong and causing them to back down). A captured German officer, asked what stood between his force and success, was told "Divisional headquarters." A small cluster of administrative staff, whose job is normally to plan battles and order supplies, were the last line of defense.
The Battle of the Alamo in 1836.
The Netherlands in World War II. In 3 days, when the first defenses reached the border, the German forces were already in the middle of the country. This happened mostly because the classic Dutch strategy of flooding part of the countryside provides an excellent defense against land-based troops - but the Germans had paratroopers. Oops.
Similar the invasion of Denmark during which German forces crossed the border in the early morning and paratroopers took control of the Danish air bases. Some hours later German bombers dropped leaflets over Copenhagen, which pretty much said "All your base are belong to us!", and by noon the government had surrendered. The trope was played even more straight with the simultaneous invasion of Norway. Oslo's impressive naval defenses kept the German navy at bay for long enough to secure the kings escape into exile. Once he was safely away, the troops surrendered. Or retreated into hiding.
Aided by extreme boldness of the Germans. On the first day of the invasion of Norway, only a few dozen paratroopers and a recon plane who landed at the airport were the only Germans in Oslo. But, within hours of landing, these guys were holding a parade on the streets of the capital that convinced the Norwegians that a much larger force had landed and has successfully gained control of the city.
Sometimes All Your Base can be an advantage: at one point during the Seven Years War, the Austrian army took advantage of the Prussian army's absence fighting the French to capture the province of Silesia. When the Prussians eventually responded it was to discover they were outnumbered 2:1 on a battlefield of the Austrians' choosing. Unfortunately, the site they had chosen near Leuthen happened to be the Prussian Army's peacetime training ground, and the resulting familiarity with the terrain made the Prussian victory almost hilariously one-sided.
And then the Austrians did the same thing to Napoleon on the Marchfeld.
During World War II the Royal Navy pulled one on the Italian navy with a torpedo plane assault on the Italian fleet in Taranto's harbour, disabling three battleships and showing to the world that the raid on Pearl Harbor was possible (both Taranto and Pearl Harbor having water shallow enough that the use of aircraft-launched torpedoes was thought impossible).
During World War I Italy had proto-Fascist Gabriele D'Annunzio, who pulled it twice: first time he led a torpedo boat raid on the Austrian fleet in the harbour of Bakar and left a mocking message (it doesn't count as the Crowning Moment of Awesome both because the Austrians placed torpedo nets to further protect their ships and later an Italian torpedo boat would sink the Austrian flagship after accidentally meeting it on patrol), and then he led a flight over Vienna to drop propaganda leaflets just prove they could bomb the enemy capital if they just wished so (cue Oh Crap for Vienna's people).
The Italian Navy's Crowning Moment of Awesome during World War II was one of these: with some of the original manned torpedoes, the Italians penetrated Alexandria harbour and mined two battleships (including the flagship with admiral on board) and a tanker (there was no carrier, so they mined another target), disabling the battleships and damaging the tanker and a destroyer (collateral damage).
In the Battle of Agincourt in 1415, the English returned to their base after kicking French butt and discovered that a small group of French knights had slipped past them during the fight and killed the guards watching over their baggage. This episode is recreated in a scene in Shakespeare's Henry V.