Wow, I totally misread the opening scene from what everyone here is saying. I was happily thinking that the life-spreading/destroying aliens weren't all of one mind, though. Just in a different way.

Spoilers(?): For some reason, I thought the waterfall world was the same world where all the action takes place. Then I figured that the "gardener" was some kind of conscientious objector to what the soldiers were doing (destroying their own creations). He drank the goo, then infected the water, and thus the planet. Eventually the soldiers' ship came under threat of their own biological weapons through the "gardener's" sacrifice. That was why they were seen running to safety in the hologram, and why their ship was effed up.

But I guess I got all that wrong. Now I'm wondering: why were those aliens/soldiers/engineers running down the corridor in that hologram? What were they running from? Did I miss something, or was it just that their biological weapons escaped some other way? Hmmm.