There's an area shown on the map in the light zone that is called "New York Office of Emergency MNG". It has a large circle around it and a label that says Secure. Maybe that's where the extraction goes. Another option that is less likely is that the game kicks you out to an instanced "Safehouse" that you can store items and sleep or bandage your wounds. Very unlikely but would be pretty cool
It seems like extractions would be carried out by a heli from base camp, which seems to exist.
One thing I am curious about is how it appears there are multiple factions, does this mean there are competing agencies or something? What is the motive for them to be shooting each other? Can't wait to find that out.