When you fire a missile all of its guns are expended against a single target and the missile is destroyed.  A missile must be unloaded from a carrier on the turn it is fired.  You can explicitly unload a missile before you fire it, but if you fire a loaded missile the game server conveniently issues an automatic unload command for it first.  If a missile is unloaded and not fired on that turn, it must be reloaded on a subsequent turn to be used. 
 
Note that firing a missile is not the same as firing its carrier guns.  That is, a loaded missile can be fired, leaving its carrier free to move to another sector in a "hit-and-run" attack.
 
It is possible on the same turn to unload one missile, load a second missile in the same rack space, and fire both missiles during the Combat phase.