A long standing claim from conspiracy theorists has been that the United States military had a copy of the space shuttle all its own. So does the military fly secret missions to space for the purposes of defense and reconnaissance, or possibly even to deploy weapons on enemies during times of war?
Based on the best available evidence, it does not seem likely that the military has such an spacecraft. However, that does not mean that the military does not use the shuttle fleet for military missions, or that such a craft is not in the works.
History of the Military Space Shuttle Program
When the current fleet of space shuttles were being developed it was planned that additional copies would be built exclusively for military purposes. This fact led to certain specifications of the shuttle design being expanded, such as the amount of glide time of the craft.
Ultimately, it was determined that having dedicated shuttle craft for the military was unnecessary. Given the amount of technical support, staff and facilities required to run such a program it made more sense to use other resources to launch payloads into space. Instead more sophisticated spy satellites were developed to accomplish reconnaissance missions.
Use of the Shuttle Fleet for Military Operations
Without its own fleet of shuttles, the military has relied on NASA's vehicles to meet its needs. In fact, the space shuttle Discovery was planned to be available to the military as their exclusive shuttle (with civilian use as it was available). It was even going to be launched from the military's Vandenberg's SLC-6 launch complex. Ultimately the plan was scrapped following the Challenger disaster.
Instead the military used whatever shuttle was available at the time of need, and was launched from the usual launch pad at Kennedy Space Center. The last shuttle flight strictly for military use was carried out in 1992 (STS-53). Subsequent military cargo was taken up by shuttles as a secondary part of their missions.
As it turns out, it isn't necessary for military cargo to be carried aboard shuttle craft. With the increasingly reliable use of rockets, the military has a much more cost effective means of ferrying objects into low Earth orbit.
Since the military can use standard rockets to meet their needs, or use one of the normal shuttles if absolutely necessary, the military really has had no need for its own craft. And given the immense expense it would require to maintain the facilities, personal and hardware to run such a program, it seems highly unlikely that such a program exists.
Will the Military Ever Have Such a Shuttle Program?
While the military hasn't had a need for a conventional manned orbiting vehicle, there are situations that could call for a shuttle type craft. And with the retirement of the current shuttle fleet, the military is preparing such options.
However, these craft will be quite different from the current stable of orbiters; perhaps not in look, but definitely in function. The X-37 shuttle was originally designed as a potential replacement for the current shuttle fleet. But once NASA and the government re-examined the goals of NASA it became clear that an Apollo type craft would better fit their needs.
As a result, the development of the X-37 was taken over by the Department of Defense (DoD), culminating in the X-37B which had its first successful flight in 2010. This craft, unlike the current shuttles, is unmanned, and will likely take on more of a reconnaissance role, rather than a delivery system to low Earth orbit. (Though it will have a small cargo bay, capable of taking small satellites into space.)
There are other glider type aircraft being developed by the DoD, but these systems are being designed as high altitude hypersonic craft, and won't actually reach orbit. But clearly the military is interested in the ability to place objects into orbit as well have reusable, spy craft so expansion of projects like the X-37 seems entirely possible.