The T3 strategic missile defense, SMD for short, is a stationary structure with the sole purpose of launching ordinance to intercept incoming hostile strategic missiles (nukes). They will not intercept friendly strategic missiles: launched by yourself or by allies.
These units must be ordered to build their ammunition. Once built, the missiles will be stored until needed, and will be lost if the SMD is destroyed. Because of this, it is often inadvisable to build more than two defensive missiles in any one structure, unless you anticipate multiple incoming launches. One SMD can defend against up to five simultaneous incoming launches, if stocked with enough ammunition. SMDs can intercept strategic missiles targeted outside their operational radius when flying overhead. It is also important to note that the splash damage from a strategic missile detonation just outside the SMD's radius may very well damage or destroy objects within the periphery of its protection area.
If you find your SMD being spefically targeted, an incomming nuclear strike is likely.