We're talking race 5. Looking at the shadowy blob in the I would guess they're like the 'anomalies' from S.T.A.L.K.E.R. and must be killed by some special means. The bipedal figure is some evil leader that can control the blobs.
Alternatively,
They are all bipedal, and have a shadow-disperse when they get shot at for self-defense. They poof around in battle to get behind you and attack.
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That bipedal figure does appear to have horns or something on his head...of course the pyramid ships are a dead giveaway that they're bad. I mean...what GOOD has ever come from dark pyramid ships?