The Maguar and the aliens fighting them in Figure17 are confined to rural Hokkaido.
In Code Geass, one would have expected the capital of Britannia to be somewhere on the North American eastern seaboard, perhaps in one of the original thirteen colonies or the other Britannian (British) New World settlements. Instead, it's located in the middle of Arizona, either around where Yuma (as it was located on a map) or Phoenix (going by the surrounding mountains and southwestern desert landscape) would have been.
Dominion Tank Police takes place in a heavily polluted, killer cyborg infested, futuristic version of Newport, Rhode Island.
In Halo: Uprising, when a captured UNSC Soldier is tortured by the Covenant, he tells them the "Key of Osanalan" is in Cleveland. It was a ruse to keep them from glassing the city where his brother was living.
In Gold Digger, the Diggers family lives in Atlanta, Georgia. Consequently, all the supernatural and superscientific friends, enemies, and acquaintances they make during the course of their globe-trotting and multiverse-hopping adventures inevitably end up finding their way there.
The Jaime Reyes runs of Blue Beetle deviated from the standard "stick the hero in a counterpart of a real-world city" DC formula by having Jaime patrol El Paso, Texas.
In the 4-issue Great Lakes Avengers series, Maelstrom manages to create his universe-ending device successfully, and has only the titular D-List team to face him. He notes that he succeeded in creating his doomsday device because he didn't go to a major city like Los Angeles, London, or New York, but instead went to Milwaukee, Wisconsin!
Pretty much the whole point of The 50 State Initiative. A super Hero team for every state, even Iowa. And of course, our friends The Great Lakes Avengers patrol Wisconsin as The Great Lakes Initiative.
Rom Space Knight: a major center of the Dire Wraith invasion is Clairton, West Virginia.
Eduardo Risso's (with scripts by Barreiro) "Parque Chas" turns this into a joke, setting a detectivesque comic writer in the very quiet, middle-class, small and residential neighbourhood of Parque Chas, in Buenos Aires, where a lot of crazy paranormal stuff is going on due to a dimensional gate. The craziest part is that there are indeed urban legends about Parque Chas, due to its weird circular streets.
The Mirage Teenage Mutant Ninja Turtles run into all kinds of supernatural crap. It's easy to overlook when they're in New York, but it feels jarring when they're constantly running into aliens and eldritch abominations in Northampton, Massachusetts.
Secret Avengers: The secret empire has built their underground teleporting city beneath Toledo, Ohio for two reasons: It has no subway systems and there is very little chance of any government or media attention.
The new Ms Marvel is Jersey City's very own (well, only) superhero.
In Worldwar: War of Equals, the aliens do land near or outside capitol cities such as Sao Paulo, Cairo, Kiev, Beijing, and Mumbai, they also choose to land in some place that aren't so popular such as Belleville, Bari, Al Basrah, and Bendigo.
In Close Encounters of the Third Kind, the aliens are first spotted in the town of Muncie, Indiana. They land at Devil's Tower, Wyoming (the mountain Roy keeps trying to sculpt.)
Alien vs. Predator: Requiem takes place in the small college town of Gunnison, Colorado, about as far out in the sticks as possible. The movie exaggerates, however, making the town several times larger than it really is, and giving it a power station and other such accoutrements (it was actually filmed on Vancouver Island, Canada).
In Star Trek: First Contact the Vulcans first land in Montana, though they had a pretty good reason as they were looking for the people who managed to create spaceship with warp technology in their basement. This is a case of Author Appeal: Brannon Braga is from Bozeman; he even named a USS starship after it.
Starship Troopers: The first city attacked by the aliens in Buenos Aires, which happens to be our hero's hometown.
Discussed in The Faculty. When one character points out the absurdity of aliens secretly invading via a High School in small town Ohio, another Genre Savvy character points out that it'd be easier to secretly invade in somewhere out of the way than try to blow up The White House, which the whole world will notice.
Lampshaded in the first ten minutes of District 9, where the sick, malnourished aliens had the misfortune to make first contact with Johannesburg, and notes when the ship first appears over the city that it wasn't some place like New York, London, or Chicago. Cue thinly-veiled apartheid parallels.
Claire: "I asked myself, where would people never notice a town full of robots? *mocking gasp* Connecticut!"
In this short film Ataque de Pánico! (Panic Attack!), aliens destroy Montevideo. Where? Why it's the capital of Uruguay of course!
Thor: upon being stripped of his powers, Thor lands in a small town in New Mexico; and his hammer, Mjolnir, in another location 50 miles away from his. Dr. Jane Foster and her colleagues seem to take this in stride; as Thor has trouble adjusting to Earth customs.
Attack the Block has aliens landing in London, but it's not exactly the postcard version.
Dimples: "What kind of alien, out of all the places in the whole wide world, would invade some shitty council estate in south London?"
Dennis: "One that's lookin' for a fight!"
Looper is a hardboiled, time-traveling hitman tale set in... Kansas.
In Incident At Raven's Gate, aliens invade a small town in South Australia.
In Bruges, which takes place in "fuckin' Bruges," was chosen because the protagonists are laying low and it naturally makes sense as a result. However, since Bruges is relatively unknown in real life too, the characters frequently question where it actually is.
Dude Wheres My Car: "We will now use the power of the Continuum Transfunctioner to banish you to Hoboken, New Jersey!"
Ford: Teasers are usually rich kids with nothing to do. They cruise around looking for planets that haven't made interstellar contact and buzz them . . . They find some isolated spot with very few people around, then land right by some poor unsuspecting soul whom no one's ever going to believe and then strut up and down in front of him wearing silly antennas on their heads and making beep beep noises. Rather childish really.
The first Martian ship to reach Earth in The War of the Worlds lands in Horsell Common in Woking, Surrey. Orson Welles' radio production, and many subsequent adaptations, move it to Grover's Mill, New Jersey.
The small town of Illium, NY, is where the world-destroying substance Ice-9 is developed in Kurt Vonnegut's classic Cat's Cradle.
This trope is openly discussed by Stan and Pete in How To Build A Skydeck, set in the small town of Columbus, Georgia.
Daniel Pinkwater likes setting the weirdness in his books in odd places like Hoboken (The Hoboken Chicken Emergency) or other obscure towns (Yobgorble: Mystery Monster of Lake Ontario). And that's when the weirdness isn't happening in Hogboro.
In Roger Zelazny's Doorways in the Sand, the rogue terrorist threatening the world (or at least threatening the world's good relations with its new alien friends) does indeed turn out to be Australian.
The Captain Underpants series takes place in Piqua, Ohio, a real city with a population of a little over 20,000.
Good Omens has Lower Tadfield, an unremarkable village somewhere in rural (probably) Oxfordshire, as the location of Anti Christ and start of the Apocalypse.
The first scouting sortie of the alien collective in Alan Dean Foster's A Call to Arms encounters as its first human contact a musician in a fishing boat off the coast of Belize.
The events of Scott Westerfeld's Midnighters trilogy takes place in Bixby, population: 13,000. Though the location is important to the plot.
The Chrysalids portrays a surviving enclave of civilsation after an implied nuclear holocaust. Naturally it's in Newfoundland (althought New Zealand seems to be doing pretty well too.)
Twilight is set in Forks, Washington, a place the residents have barely heard of. Another vampire clan lives in Denali, Alaska. Considering they've been there for a while and how rural, scenic and insular these places are, this may also overlap with Lovecraft Country.
In the novels of the Black Dagger Brotherhood, the largest vampire population—and the headquarters of the eponymous secret society—is in Caldwell, NY. Yep.
The Mercy Thompson series of books, sure people know OF the Tri-Cities in Washington, but few can name all three, and remember this is three cities that take up the same amount of mileage as the ONE city that Washington is known for.
Robert J Saywer’s Calculating God: The aliens want to take a good look at Earth fossils, so they go to the Royal Ontario Museum in Toronto.
His Neanderthal Parallax books have a Neanderthal from a parallel universe appear in...Sudbury, Ontario. Sort of justified, since the device that sent him there was built in the same cavern as the Sudbury Neutrino Observatory. You may have guessed by now that Robert J. Sawyer is from Ontario.
In The Kane Chronicles, Set initiates his plan to take over the world, obviously starting in New York, right? I mean, that's where the heroes are based and that's where the last group of evil gods started their attack. But no, he starts with Phoenix, Arizona.
Richard III in the 21st Century comes to call Portland, Oregon home after his initial trip through time there. Other important scenes take place in Rochester, New York, and the Big Applesauce shows up as a location only because of the justified use of New York Presbyterian-Columbia University Hospital as the site of some very specific medical research.
S. Andrew Swann's Dragons of the Cuyahoga duology has a portal to a magical world open in Cleveland, and dragons, elves, dwarves and such come through, along with magic (limited only to the greater Cleveland region).
Ever since the show returned in 2005, it made Cardiff, the capital city and most populous county of Wales and the headquarters of BBC Wales (the producers of the show), a Weirdness Magnet courtesy of a dimensional rift. This trope is repeatedly lampshaded by several characters in both Doctor Who and Torchwood by their dumbfounded reactions to the thought of supernatural stuff happening in Cardiff. While the Doctor only visits Cardiff on occasion (to "refuel" the TARDIS) the first two series of Torchwood are set there.
Even gets lampshaded during Season 2 when Gwen tries to tell Rhys what she really does at work. His reaction is (obviously)"Aliens?? In Cardiff??"
When Doctor Who stories are set in America, they either take place in New York, Washington, the area around Cape Kennedy, or... Utah? Utah's importance is due to the unusual properties of the location and time for them to create a fixed point in time and space in an attempt to kill the Doctor.
In an Eleventh Doctor audio story called 'The Ring of Steel', the aliens invade on Orkney, a small group of islands off the north coast of Scotland. Justified as the aliens in question were genetically engineered to survive by converting planets' atmospheres into hydrocarbons and eating the life trapped 'like flies in amber', but wish they didn't have to. Therefore, they choose somewhere quiet and out-of-the-way to invade in the hope that no one will notice.
An episode of My Hero had Thermoman stop an abandoned Russian space station from crashing into the center of Grimsby.
In fact, Cleveland is rather frequently a subject of this trope, hence its alternate title, Aliens In Cleveland. It's part of a long-Running Gag in popular culture that Cleveland is a depressing hellhole of decay, corruption, and a river of fire. The city's demonic influence permeates into its residents, who actually like it there.
The Roswell episode of Star Trek: Deep Space Nine had Nog fabricate a story about alien conquest of Earth, randomly pointing to the initial landing site on a map (next to a 'blue blob'). The soldier who is listening to him leans in and exclaims, "Your people are going to invade... Cleveland???"
One of the 'unseen' scenes from Harry Hill's TV Burp parodies an occurrence of this in some drama or other; a long list of cities scrolls past, from "Lagos", "New York", "Tokyo", and then the map zooms in and the final location affected is revealed: "Norwich". Harry starts to go into a panic: "But where will we go to see puppet dramas without the Norwich Puppet Theatre? And where will we buy our many varieties of mustard when The Mustard Shop is destroyed? Oh no!" (Aside Glance) "I'm kidding. I love Norwich!"
It's Eleventh Hour. They were listing cities that would be destroyed by rising sea levels. The paradox was that they wanted to list a British city for impact but retain scientific accuracy, and that was the narmyresult.
In the pilot of Star Trek: Enterprise, an interplanetary incident is set off when a Klingon crash-lands in Broken Bow, Oklahoma.
Midway through season 7 of 24, Colonel Dubaku targets a pesticide plant just outside Kidron, Ohio (pop. 30,000), for his next terrorist attack.
Being Human has vampires planning a vast global empire from their headquarters in Bristol, England.
Lampshaded by George, who directly asks the question of 'Why Bristol?'
And later, in season 3:
Mitchell: It can't happen like this! Not here! Not in WALES!
Charlie Jade takes place in three alternate universe versions - one dystopian, one ecotopian and one normal - of Cape Town, South Africa.
Heroes goes all over the place. The most prominent cities are major population centers (New York, Tokyo, Los Angeles), but plenty of other locations are visited. Claire Bennet (and one of Primatech's major facilities) is in Odessa, TX. The Volume Three finale is set in Hartdale, NY and Fort Lee, NJ. The plane carrying all the heroes at the start of Volume Four crashed in Oklahoma.
3rd Rock from the Sun is set in Rutherford, Ohio. The place is fictional, but it's obviously meant to be a typical Midwestern town.
A season of 24 features a significant plotline involving terrorists in Palmdale, California, a mid-sized city a couple hours outside of the greater LA area. It's justified by the fact that the terrorists are hiding out and intend to target major cities when they're ready. It's also small enough to get nuked without completely changing the world in which 24 takes place.
True Blood, and obviously the Sookie Stackhouse novels the show is based on, are set in Bon Temps, a fictional suburb of Shreveport, Louisiana. Dallas and Jackson, Mississippi have also been significant locations.
Stargate SG-1 tended to use this for its Earth episodes. The frequent use of Colorado Springs is justified by being where the main cast actually lives, being the closest city to the Cheyenne Mountain installation. Those examples tend to be a case of the cast being Weirdness Magnets, for instance an ascended Ancient falling in love with Carter and following her home. Other examples include a rural area north of Seattle ("Seth"), and Steveston, Oregon ("Nightwalkers").
Charlie Daniels' "The Devil Went Down To Georgia." Although it is mentioned that he was "way behind" and getting desperate.
Subverted-by-Real Life example: The designers of Shadowrun originally picked Seattle for their game's home base, because as large North American cities went, it was relatively obscure in pre-90s pop culture. Little did they suspect that movies, TV shows, grunge and Starbucks would conspire to elevate Seattle's cultural prominence in the years to follow.
In Half-Life 2 the office of the entire planet's military administration is located in a small city at the Black Sea (unless it's in Latvia. Or northwestern Russia. Or Somewhere). Which coincidentally is exactly the same place where the few survivors of Black Mesa have created their secret rebel headquarter. Though it might have been the cities exceptionally high rebel activity that caused the administration to relocate there.
Any level in the Halo series that takes place on Earth is set in Africa, specifically New Mombasa and Voi. However, one of Earth's space elevators is located in New Mombasa, making it less Cardiff and more Rotterdam (one of the largest ports in the world).
It's also the location where The Forerunners build the portal to the Ark, and also located right next to the area where the first modern humans originated.
Played for laughs in an Interactive Fiction game, where part of the backstory details Satan's arrival on Earth to punish humanity for their sins and his construction of a hellish citadel to house his legions in New Jersey. Apparently it was a few years before people realized something was wrong.
In MDK, the population centers threatened with annihilation by the invading city minecrawlers were Laguna Beach, Lindfield, Livingston, Kirkaldy and Sparrow Pit. In MDK 2 the city minecrawler in the opening mission was targeting Edmonton.
In Persona 4, it turns out that the identity of the Gas Station Attendant was Izanami, Goddess of the Underworld, who had been responsible for bestowing Adachi, Namatame and the protagonist the Persona of Izanagi, giving them powers to enter the Midnight Channel and created the being responsible for the fog. And all this is done from Yasoinaba, a town considered out in the "boonies" in Japan.
Earth made its first real appearance in Mass Effect 3, something that was heavily marketed in the game's advertising. Namely, the Reaper attack on London. However, the first we see of the Reaper invasion is the scorched remains of... Vancouver. Justified in that Bioware is Canadian and Vancouver is one of Canada's largest and most famous cities, and averted in the final battle, which takes place in London.
In Metal Gear Rising: Revengeance, the entire middle of the game takes place in Denver, Colorado. Not exactly a small city, but definitely not the first to come to mind.
In an It's Walky! storyline, Head Alien experiments with his new time freezing technology in a small town in Canada, leading to the exchange in the page quote. It's also an excuse for a Cross Over with another webcomic, Avalon, set in small-town Canada, which was in the middle of a long hiatus.
In the flash series 21 (a parody of 24), plumber Al Johnstone has 21 minutes to save Norwich from a nuclear explosion.
Although a very populous place, there are not many superhero stories that take place place in Germany's Ruhr Area, a fact that was one of the motivations of Ruhr Area native Arne Schulenberg for creating Union of Heroes.
Spinnerette features superhero action in Columbus, Ohio.
The main setting of At Arm's Length and seemingly main magical entrance portal to Earth Houston. Apparently monsters like to target Hermann Park.
The PPC's main base in the real world (or "World One") is a city in New Caledonia, a French overseas territory. Nobody is quite sure why, though there are other doors to HQ scattered about Earth and the multiverse in general.
Brental Floss' Civilization song includes the line "learn to write before you can read and build the Taj Mahal right in Cleveland".
An episode of The Tick animated series featured a bunch of supervillains known as "The Swiss". Who were dressed in uniforms bearing the Swiss flag and wielded giant Swiss Army Knives:
Die Fledermaus: Listen to me! The Swiss are invading The City! American Maid: Switzerland is a neutral country, you goober. Die Fledermaus: [showing his arm in a cast] YOU CALL THIS NEUTRAL?
Vlad from Danny Phantom lives in Madison, Wisconsin. He's a Green Bay Packers nut.
In Megas XLR a giant mecha ends up in Jersey City, leading to all manner of hijinks and invasions.
Lilo & Stitch has the epicenter of alien activity on Earth in Hawaii—it's not even on the most populated island, but Kauai. The fact that there weren't any major cities on the island was a plot point: Stitch can't swim so he wasn't able to immediately commence with the mass destruction he was built for; he pretended to be a dog so he could manipulate someone into getting him off the island.
Apparently the original idea was for Stitch to crash-land into a very rural area of Kansas. Possibly, they changed it to cover the aforementioned issue of why he couldn't just walk to another city.
Alien invasions were the order of the day in Terlawk, New Jersey on Earthworm Jim. Justified in one episode where it's revealed that one of the town's residents used to work for NASA, and spray painted "Hey aliens! I dare you to attack Terlawk!" on a satellite.
In the Danger Mouse episode "Multiplication Fable" DM and Penfold investigate a spaceship crash landing in Birmingham, England.
The events of Roswell, New Mexico come to mind. Aside from the odd military base, the closest notable landmark are the Carlsbad Caverns, and even that is a bit of a stretch.
Of course, Roswell is now a landmark, but that's because of the landing more than anything else.
Following WWII (and at the time of the Incident) Roswell was the home base for the 509th Bombardment Wing, the world's only nuclear strike force. Which almost certainly has nothing to do with the Incident, but it makes great conspiracy theory fuel.
It is also worth noting that Roswell is where Robert H. Goddard, a founding father of modern rocketry developed and tested rockets in the 1930s. A local high school is named in his honor.
Given that it was a facility for rocket testing, locating it as far away as possible from anything was most probably intentional.
Bonnybridge in Scotland has an average of three-hundred U.F.O. sightings per annum, earning it the nickname "U.F.O. Capital of the World" despite the fact it's a fairly obscure town (even in Scotland).
The Flatwoods monster/alien that was seen in Flatwoods, West Virginia, in 1952. The town has a population of 348.
The stereotypical monster/alien sighting is the redneck who lives out in the middle of nowhere.
A non-alien example, but when the Live 8 concert locations were announced back in 2005, with concerts in places like London, Paris and Berlin, Canada's concert venue was held in Barrie, a cottage town about 60 miles north of Toronto. This was much to the bemusement of many, particularly residents of Barrie.
For that matter, the original Woodstock concert took place on a dairy farm in the Catskills near Bethel, New York. Most of the area's few thousand residents felt the same way about its attendees and performers as they would have about alien invaders.
The Tunguska Event, largest asteroid/comet impact in recorded history, was in the middle of nowhere - fortunate, given had it hit a city it would have leveled it. Of course, conspiracy and fringe theories about the cause abound.
The Niihau Incident, during WW2. One of the Pearl Harbor bombers crash-landed on the Hawaiian island of Niihau, believing it to be uninhabited. The island is privately owned and access is restricted, but a tiny community who still speak the native Hawaiian language are allowed to live there. The Niihauns, who could not communicate with the outside world, were left to deal with the Japanese pilot all by themselves.