I'd be lying if I'd said that I fully understood the aliens in this game, but I still like to think that some of them (the ones that aren't being controlled by their overlords) may be having second-thoughts about wiping out the humans and may actually want to help humanity. In this case PHALANX would benefit from rescuing the defector (boost to research and possibly a new branch of research) before it's former comrades and/or over-zealous humans get to him.
