The C.H.U.D. live under Tokyo!
The Japan Times Online reports:
Shun Akiba, a former high-level foreign reporter, has identified hundreds of kilometers of Tokyo tunnels whose purpose is unknown and whose very existence is denied ... Shun claims to have uncovered a secret code that links a complex network of tunnels unknown to the general public. "Every city with a historic subterranean transport system has secrets," he says. "In London, for example, some lines are near the surface and others very deep, for no obvious reason."
With Shun's book now in the fifth edition (though unfortunately not yet translated into English) there's been talk of these tunnels before, such as on the excellent BLDGBLOG, where one comments about the ill comparison to London:
[London's] subsurface tubes are limited to the earliest lines. It's very disruptive to build a subsurface tunnel; the District Line along the Thames, for example, was built as part of a wholesale redevelopment (the Victoria Embankment) which also included sewers and roads ... Of course, some lines are a bit deeper than others, but that's usually determined by a mix of interchanges (can't have two tubes at the same level, unless they're parallel) or geology (you want good clay, which is also the reason the Tube didn't impinge much on South London).
Another comment on a private mailing list suggests the... oddness of a country building nearly 1500 kilometers of unmapped tunnels in an earthquake-ridden city, where one would expect constant destruction and decay. (And did you lose the C.H.U.D. reference? You've missed an excellent movie, but stay away from the sequel!)