This related question details some of the military missions of the Space Shuttle. My question is about the training for these missions. Some aspects of all Shuttle missions are largely the same, and it makes sense that much of the training for military missions would occur as with other missions at the Johnson Space Center in Houston. However, there are certain aspects that are mission-specific. Was the mission-specific training also done at JSC in Houston, or was it done off-site (e.g. at a military base)?
It was done at the Johnson Space Center, in the regular training facilities.
The Shuttle Mission Simulator (SMS), for example, (the one I am familiar with) had the capability to run each simulator in "red" (classified) or "black" (unclassified) mode. To go from a classified mission's "training load" to an unclassified training load was called a "color change" and took about an hour as DOD-approved memory clearing software had to be run on all the computers associated with that simulator.. (A normal load change took less than 15 minutes).
The SMS was kitted out with all the usual appurtenances of classified facilities - a guard at the door 24/7, a secure vault with Faraday cage walls, etc. We all had to have secret clearances, but "need to know" definitely applied. I well remember having to go to the vault to get hardcopies of displays dealing with completely generic simulation model problems such as hydraulic heaters not working right, etc - but since the launch times for the classified missions were classified, and all the displays had time & date at the top, therefore all the hardcopies were classified. I had to sit there in the vault and get the info I needed off the hardcopies.
The Mission Control Center had to deal with the same dual-mode ops situation.
This slide is the only references I can find to back this up. It's from a pre-Challenger-accident presentation that describes the facility. "Controlled mode" refers to secure operations, and I've drawn a red box around a reference to DOD mission training.
The entire presentation is available at the Shuttle Mission Simulator Facebook page (Facebook login not required to view), but since I'm the one who posted it there, it does not provide much in the way of independent verification.