You start the mission close to the hangar, where you saw the Metal Gear during the cutscene. First of all, return to the red door into Serak Power Plant. You need to sneak across the plant and it is recommended that you take the same route as previously, i.e. right next to the rocks on the right. There should be not much trouble avoiding the enemy soldiers, but you need to watch out for the gunship with a spotlight patrolling this area. Take cover or drop onto the ground as soon as the enemy vehicle starts checking the area around you.
Note - You can shoot down the chopper. This would make exploration of the HQ easier, because the chopper will reach that area along with your character. Do this only if you have taken along a good rocket launcher with automated targeting system and is capable of destroying it, or dealing severe damage, in one hit.
After you leave the power plant, you need to head North-West towards Afghanistan Central Base Camp. Along your path, walk around all of the enemy outposts. Apart from that, do not move too fast and try to stay away from the main road, because it is being patrolled by, at least, several enemy groups, several soldiers each. It is best not to take the risk and save up on your supplies, instead of taking on the opponents in your way. After you get close to the enemy HQ, leave the main road and climb the hill on the right, which provides you with a good overview of the camp.