Show theory 2

As I said in my previous post, what if they crashed the juggernaut? Causing life threatening ingries to Shaw and Davids only way of saving her was to put her in one of the engineer pods. In order to function correctly he had to put a pressure suit on her.

This whole time David finds the engineers and considers him far more superior then them and releases the black goo on them. The environment and the engineers will be evoluving/ mutating in this time period. David unleashes hell upon the covenant crew and his "creations".

When they realize that its davids fault , the remaining survivors go after him. Including Walter. They chasing him back to the jaggernaut where they corner him. He will be damaged from the bullets, aliens, etc.

He manages to get ahead of the covenant survivors closing the door to the engineer chamber buying himself some time. Baddly damaged he grabs one of the erns containing the black goo. He opens the sleeping pod door where Shaw is sleeping.

Walter manages to figure out how to open the door. Just as their running in to finish him off. He opens the ern (while standing over shaw) but they shot it out of his hands. The ern goes up in the air and opens up completely falling over him, mixing with his android biology. 

He drops to his knees as the black goo and his fluids fall upon Shaw. Now remember Shaw has the pressure suit on. David gets up and goes haywire. Mutating into something new while he is fighting with the survivors. Walter would really be his only match, causing him to sacrifice himself to kill David. Shaw is awoken from the pain.

The black goo and Davids android fluids cause the biosuit she is wearing to mutate her into a superiorform of all the  xenomorphs. She manages to escape. Mutating along the way.

As they search for her , the remaining  neomorph, protomorphs sense her presence and protect her. Remember in Prometheus she had the trilobite? Her transformation causes her to become the queen...