The Engineers were trying to create an army of ALIEN XENOMORPHs, the creature you see bursting out of the Engineer's body at the end of the show.
Human/Engineer DNA combined with the Giant Squid creature is required for this. The giant squid would enter a human orally and after a few hours, an Alien Xenomorph would form and burst out of the human body.
In order to mass produce an army of Alien Xenomorph, The Engineers sacrificed a single Engineer knowing that in time, his DNA would populate the Earth with billions of humans.
Humans they needed to fuse with the Giant Squid and create Alien Xenomorphs.
The Engineers would visit Earth from time to time to check the population count.
Finally, on the day when they were about to come back to earth with their black biological liquid (the black liquid that transforms earthworms to snakes, reanimate corpses, causes mens sperm to impregnate women with baby alien squids) and farm an army of Alien Xenomorphs from Humans + Squids, something happened on board the Engineers ship that prevented this from happening.
From here, the show carries on the tale… Prometheus…