While fighting The End, climb a tree onto a ledge that is easily accessible to the old man. Lay down and take out your sniper rifle, go into first person, and search the trees, not necessarily looking for The End. You will eventually hear his footsteps behind you, but do not turn around. You will get a short cut scene where The End finds you and shoots you one with his rifle. Instead of killing you he says that you don't deserve to die that easily. He then proceeds to pick Snake up and carry him to the nearby jail where he will eventually awaken.