Extracted the Skulls
You can't accomplish this secondary objective during the first playthrough, as the main character is unable to extract Skulls during this mission. As this ability is unlocked just as you finish the twenty-ninth mission, you can just repeat it as soon as you complete it for the first time.
Members of the Skulls unit can be attacked with any equipment, even the one that allows you to drain their health bars (such as the sniper rifle, rocket launcher, grenades, etc.). After you've defeated a member of the Skulls unit, he will drop on the ground and lose consciousness. You can then go to the enemy (if the area is secure, that is) and fulton him.