If it's hostile, you kill it.

The standard, canonical ending - you let the missiles destroy the Dark Ones. It's the default: if you haven't banked enough moral points, or you simply don't shoot the guidance control at the final tower, you get this one. Easy to get by just playing to the finish. Mutually exclusive with Enlightened in a single run, so the clean approach is one careful moral playthrough for Enlightened and a fast replay (or an end-game reload) for this.