In a way Ridley Scott and Damon Lindelof weren’t lying when they told members of the press that Prometheus isn’t a prequel to Alien. The two movies actually have very little to do with each other, as there are no recurring characters, ships or even really aliens. As a result, it’s hard to identify the film as a traditional prequel, as there are no huge, moments where you realize that the stories are crossing over. But while Prometheus’s connections to Alien are slim, they do have one very important element that links them together, and that element is evolution...
When we first see what we know now as xenomorphs in Prometheus, they can’t be recognized as such: all they are is black goo stuck in a bunch of vases. But this is simply because they are at their very earliest stages of evolution, as they begin life as single-celled organisms and slowly begin to grow. When Elizabeth Shaw and the crew of Prometheus land on LV-223 they inadvertently begin a chain reaction that leads to the earliest stages of the facehugger (first seen while Millburn and Fifield are stuck on the planet during the storm) and xenomorph.
The major chain of evolution, of course, involves Shaw and her pregnancy. It begins when David poisons Charlie with some of the aforementioned goo. Following that, Charlie sleeps with Shaw and impregnates her with an early-stage facehugger. Later in the film that same facehugger – which grows much bigger while off-screen – “mates” with an Engineer (who has the same DNA as humanity), who then gives birth to an early-stage xenomorph. These creatures, of course, would evolve further and become the highly-evolved monsters seen Alien.
The reason that this is unexpected is because everyone believed that the space jockey seat first seen in Alien was the same one featured in Prometheus. The truth is that LV-223 is not the same heavenly body from Scott’s earlier film, so not only do the stories of Elizabeth Shaw and Ripley fail to overlap, they were never even in the same place at different times.
In January 2011, when it was first announced that the project would be titled Prometheus and that Noomi Rapace would star, Scott was quoted as saying, “The keen fan will recognize strands of Alien's DNA, so to speak, but the ideas tackled in this film are unique, large and provocative.” Who knew that he was being so literal?