From what i remember scott saying is that the sj creatures existed billions of years ago and throughout the universe are old temples and "ruins" of these ancients that do the pushing and pulling of life, the sj in the 1st alien was a fossilised remnant of that ancient race that fell victim to its own creation?
I bet the only sj we see is in the intro to the movie explaining the dawn of creation etc etc.......... Either that or david the android gets infected by an organic virus that transforms him into a biomech giant that cant control his transformation ( akira style) and ends with him fusing into the sjpilots chair and somehow saving mankind by sending the derilict back 20,000,000 years and crashing it
lolz