At the end of Prometheus, why did the Engineer kill the humans? What is that thing that killed the Engineer?
The Alien you are saying is actually an "Engineer" and they developed the so called "parasite plague" to end the planet earth (which they created in the first place).
If you remember the alien or parasite plague agent that killed "engineer" was forcefully taken out by Elizabeth (Eli) from her stomach in the med pod. She actually froze it using decontamination gas of the med pod but it survived and tried to come out of that room at the end and the "engineer" was accidentally present there at the same time. The alien killed the engineer and supposedly impregnated him and that's why you see a new alien born at the end of the movie.
Check this post which gives an insight into the whole plot.