The search party splits up, and one of the crew steps on some pods, which release a spore that animates and enters his ear, where it then goes into the bloodstream. He gets sick and then hell breaks loose as an alien reemerges to wreak havoc on the crew. The landing vessel is destroyed in the ensuing gunfire and the ship is brought closer to the surface. Meanwhile, the remaining crew meet David (Fassbender), a synthetic from an earlier expedition who has survived living alone on the deserted planet for all the intervening years. He had been part of an exhibition including a doctor named Elizabeth Shaw, who had repaired him when the ship had foundered. David may have been alone for all these years but he has not been idle.
The alien finds the remaining crew in the citadel where David had taken them for shelter, and kills one of the crew. The captain, who had come to the planet with the search party, kills the alien but David introduces him to his own creations - the famous "eggs" that contain the embryonic aliens we are familiar with. The captain is infected and dies giving birth to one of the classical aliens David has engineered based on the spore virus that had been brought to the planet, and that interfaces with the DNA of the victim to give rise to one of the prototypical aliens that had crippled the search expedition.
With the captain dead, it is up to his second-in-command, Daniels (Katherine Waterston) to make sure the remains of the search expedition can get back to the mother ship, and the colonising expedition can continue. From this point the larger story of the 'vanquisher of worlds' virus is abandoned by the filmmakers, who resort to a classical "alien" battle in the ship between the humans and the creature. Needless to say, the viewer's interest in the film is diminished by this transition. It was much more interesting back on the planet, with its remnant civilisation. How did they get to the planet in the first place - those dead people whose corpses are strewn around the amphitheater - and who introduced it to that planet? And why?
It's all a bit confusing and unresolved. The Ozymandias reference is half-baked and unsatisfying. You wonder what motivated whoever it was who developed the alien virus to release it and to ruin a pristine planet. Many questions remain unanswered.