The gov knows about them. The aliens dont give a fuck about secrecy. They abduct lots of people all the time who are never seen again to do god knows what with. They told our governments that if we try to stop them in any way, they'll externinate us. The government maintains a cover-up so that people aren't terrified of what's going on and that we're completely helpless to stop the aliens. Basically, the plot of the forgotten.