Right after the meeting with Doctor Emmerich you receive information that chopper for extraction has been requested - it has landed to the South-West of Afghanistan Central Base Camp. If you have already eliminated the majority of enemies in the camp. Or if you want to end the mission quickly, it is a good idea to use the Walker Gear in the hangar. Man it and use it to pick up the scientist. Leave the hangar. If, along your path, you encounter any enemies, you can fire the machine's Gatling gun at them, which will, of course, have a negative effect on your ranking after the mission ends.
If there still are many opponents in the base, ignore the walker and carry Dr. Emmerich on your own shoulders. This will decrease the risk of any encounter of the enemies and make it easier to prevent Emmerich from taking any damage (this is required to complete the mission's secondary objectives).
Regardless of which variant you have chosen, the evacuation will fail, because Metal Gear Sahelanthropus appears where the helicopter should have been.