Japanese journalist Shun Akiba thinks he’s discoverd a secret city beneath Tokyo. There are discrepancies in old subway maps; huge swaths of land seem to have disappeared off the maps. Could the Japanese have built some sort of civil defense structure beneath the city? The United States had a number bunkers from which the government could operate in case of nuclear war, Mount Weather and the Greenbriars being the best known. Those were kept secret for some time. And I can’t say that I’m an expert in the post-war Japanese psyche, but if films such as Godzilla and I Live in Fear are any guide, announcing that huge, expensive shelters had been built to protect the Emperor and the government when bombs started falling on Tokyo might not have been a wise decision. So it’s certainly possible that these shelters were built for perfectly understandable reasons but kept classified for decades. On the other hand, perhaps Akiba is making too much of some circumstantial evidence because he really wants to believe in the existance of a secret underground city. Who wouldn’t? The Cappadocia region of Turkey has spectacular underground cities (1, 2 - links via MetaFilter); thirty-six have been discovered so far. The Parisian and Roman catacombs are true cities of the dead, hundreds of miles of ossuaries beneath the modern city streets. Pioneer-era Seattle is preserved underground. A system of delivery tunnels undergirds Chicago. Nick McCamley has documented the Cold War-era tunnels, railways, and bunkers beneath London. Whole underground societies have sprung up in Moscow (Making Light provides more information) and New York (New York’s "mole people", dwelling in abandoned subway stations, have been the subject of books, articles, and at least one documentary film). There are enthusiasts who study these places, even visit them, but "underground cities" are for the most part simply tunnels that intended were for other uses.
For the real deal, you have to turn to fiction. Edward Bullwer-Lytton (of "It was a dark and stormy night…" fame) wrote a novel about a race of subterranian superman, the Vril-Ya. William Emerson’s The Smoky God told the story of the Agharti society underneath Tibet and its capital city of Shambhala. Jules Verne’s Journey to the Center of the Earth seems to have inspired Edgar Rice Burroughs’ subterranian savage land of Pellucidar, which was first described out in At the Earth’s Core. Both drew on the idea Hollow Earth. The Hollow Earth theory was originally proposed by John Cleve Symmes, an American army captain who believed that the Arctic contained a gaping hole through which the earth’s interior could be reached. Symmes’ struggles with Congress to gain funding for his expedition before his death in 1829 are recounted in Banvard’s Folly, and he was clearly an inspiration for Poe’s Narrative of Arthur Gordon Pym.
Stories of underground civilizations were clearly commercially viable, and they rattled around for some time. Then two men, Richard Shaver and Ray Palmer, launched the modern UFO phenomenon with a single letter to Amazing Stories magazine, the "Shaver Mystery". Shaver’s letter, rescued from the trash and published by Palmer, then an assistant editor, detailed his encounters with the Deros, a race of "degenerate robots" (with robot in its loose Czech meaning of "slave") who lived in a vast network of tunnels and cities beneath the earth’s surface and used their sinister Mechs to torment humanity. Before Shaver’s story touched off a huge response — thousands wrote in to Amazing Stories to discuss their own experiences with the Deros and their benevolent cousins, the Teros — the underground societies had usually been depicted as either pockets of primitive life or highly advanced, peaceful societies. Not so once Shaver got a hold of it. It seems like Palmer believed, or at least half-believed, what he was writing (1, 2), but whether or not the Shaver Mystery was a deliberate hoax was beside the point. Shaver’s voluminous output, shaped into some semblence of cohesive narrative by Palmer, introduced a new current. They were out there, underneath our feet; they were watching; and they didn’t like us, not one bit.
Shaver continued to produce a flood of Shavernalia for Palmer’s pulp magazines. He appeared on the radio; scientists publically discussed the merits and flaws in his account. Amazing Stories‘ circulation quadrupled. But in 1947, Kenneth Arnold reported seeing some glowing discs near Mount Rainer, Washington. He reported that the flew in a wobbling manner, as a saucer would if you skipped it across water. The phrase "flying saucer" stuck in the public’s imagination. Palmer didn’t skip a beat, co-writing Arnold’s The Coming of the Saucers in 1952 and changing the name of one of his many magazines to Flying Saucer, but the thousands who had responded so eagerly to Shaver’s tale stopped looking down and began to watch the skies. "Mole people" and Roman catacombs and underground smuggling railways are all well and good, but they don’t compare to vast alien civilizations underneath the tree roots; someday, perhaps visionaries will stop looking to the stars and consider once more what’s going on under our feet.