If it's hostile, you kill it.

The default 'Ranger' ending - the canonical finish you get simply by completing the campaign without the Enlightened condition (under 50 Moral Points, or by choosing not to shoot the guidance system at the end). This is your story-complete pop, and most players earn it on their first run. If you happen to get Enlightened on both playthroughs, replay the Tower finale via chapter select and let the missiles fire to grab this.