What "secret shadow government" is there?

A shadow government is a second copy of government, a redundancy of government's essential functions but I'm not clear about which areas of government are replicated. I don't think we have a duplicate Senat and House for instance. It's existance is not a secret just it's locations, offices, staff, for security reasons in case something horrible happens. They have redundant computers on the Space Shuttle in case one goes out. There's nothing wrong with a shadow government, in theory, and maybe in practice, as long as it operates the same way and doesn't do secretive things. The US is famous for it's "transparent" government (more open than any other country I believe) where the people participate in government and everything is discussed openly in public. The "shadow government" scares some people who fear fascism.

Yes we have one:

http://news.bbc.co.uk/1/hi/world/americas/1850236.stm
http://www.abovetopsecret.com/pages/secgov.html
http://truedemocracy.net/td3/shadow/s01.html