what was all those 'running images' that the crew see?

Hi, I was wondering if anyone can help me clarify this, it has been bothering me, I don't understand it. When the Prometheus crew first come into the "engineer ship", they and Shaw see those "images of engineer running" and they follow those images. Was those images are "the engineer"? and the 2 crew that got stuck during the storm, and they found whole bunch of dead bodies before they got attack by some sort of alien worm, are those the engineer bodies? If so, who killed them? was the bio weapon outbreak? Thank you