The problem fundamentally is that so much of what we do in every way is computer-mediated. On the Internet itself it's one gigantic connected system, which was never designed to be world scale, and therefore you can get from one place to any other place and more or less do what you want with not terribly much sophistication, as such things go.
Militaries, in general, have tried to deal with that problem by air-gapping their network from the public network, and that works up to a point. But as several countries have discovered, devices such as USB keys and so on make it relatively easy to cross that air gap, and therefore military networks are not quite as separate as they are often thought of. Organizations in the intelligence world tend to be even more separate and to impose physical constraints on what you can carry across the boundary.
The threat, I guess, is things like having fighter jets show up for mid-air refuelling when the refuellers aren't there because they were told to go somewhere else, and that was done by corrupting some message somewhere inside some system. That kind of idea can be generalized in many different ways.
The trouble is that we build on an infrastructure that was never designed to be secure. Security is an incredibly difficult property to retrofit into any system, but especially computer systems, which are among the most complex things that humans have built.