The Kansas City Plant at the Bannister Federal Complex has a huge DOD nuclear facility and fits your SITE institute description. I remember recently that Kansas City was on one of Jill's lists as a terrorist target. Here are links to the facility:
http://www.globalsecurity.org/wmd/facility/kansas_city.htm
http://www.lasg.org/sites/kcp.htm
Or this also fits your description:
Posted on Mon, Jul. 19, 2004
'Secret Pentagon' hidden in Pennsylvania mountains
By STEVE GOLDSTEIN
Philadelphia Inquirer
SITE R, Pa. - Welcome to the undisclosed location.
Known familiarly to government insiders as the "underground Pentagon," this is where Vice President Cheney set up shop in the aftermath of the attacks on Sept. 11, 2001, and where he sometimes is when his office is being secretive about Cheney's whereabouts.
The location is a highly secure complex of buildings inside Raven Rock Mountain near Blue Ridge Summit, Pa., close to the Maryland-Pennsylvania state line and about seven miles north of Camp David.
A recent book, "A Pretext for War: 9/11, Iraq, and the Abuse of America's Intelligence Agencies," by James Bamford, was credited with spilling the beans about the supposedly supersecret hideaway. (snip)
http://www.kansascity.com/mld/kansascity/9189434.htm?1c
Many thanks for that info and the links Honestly.