I grew up fascinated by the X-Files. Maybe because it was one of the few shows I wasn't allowed to watch or maybe because I have always been awe struck by aliens. For those who are not acquainted with this 90's gem, the show follows FBI Agent Fox Mulder, David Duchovny without the sex addiction, and his partner Dana Sculley as he searches for the truth. In the show the government is aware of an alien invasion in 2012 and is taking precautions for it that often kill people.
Alien is similar in that the company behind the Nostromo's doomed trip gives the order to bring the Alien back at whatever expense, even if it means sacrificing all aboard to it. This is further continued in sequels.
The concept of Aliens can be scary. Whether because they are an advanced race that could easily dominate us, thank you Stephen Hawking, or a type of monster that we cannot handle. But some aliens in popular culture represent something greater. In both X-Files and Alien they represent a fear of authority and power. Both stories tell of a company/government that will kill its own people. Thus, it is a fear of authority overstepping its boundaries and keeping secrets.