Hey there!
First of all, this is a crazy, bizarre, awesome idea. This, by all means, should cost at least a couple grand to do. However, I too find this whole 'Wargames' type of mystical, dangerous OS intriguing. I'm willing to do this for a fraction of what it should cost because I think that (aside from being a headache like any other OS build) it's going to be a really, really cool venture. There are 2 paths you can take, the first being the easiest: rolling a custom Linux-based OS. We can take the Linux Kernel & basic libraries and build in our own tools capable of controlling missile silos or whatever else you want to control. We could also fully customize the interface to emulate the type of system you see in the movies. This is the cheaper option. Option 2 is to build an entirely new OS from scratch. This, in my opinion, is complete overkill. This type of thing usually takes a team months just to push out a Beta release. I could talk for hours about this, but I'll spare your time. Message me if you'd like to speak further about this. Thanks!
-Andy