After you access Nikoladze's computer, you must go out and hang from the window. After they all leave, if you only knocked out the guard when you came in, you must either kill him or knock him out again. Quickly go back to the computer to gain the information. Then, you must leave the room. Go out the door and go to your left. At this point you do not need to be silent. Go to the door that you could not open previously to find a flight of stairs. Go down them. Pick up the medical kit and use it if needed. Open the door, then jump over the railing to your left. Immediately run to the elevator shaft at the far end of the roof as fast as you can. Do the same thing as you did with Nikoladze's window -- hang down. A guard will appear and investigate. Do not worry -- just keep hanging. He will leave in a moment. After he leaves, wait a second to make sure he is far enough. Climb back up, then turn around. On the opposite side is a pole which you can go down. Jump across and grab it. When you go down, your van will be towards your left. Your van help will kill a guard. Go up and talk to him.

When at the top of the roof at the Defense Ministry -- while hanging from the elevator shaft, you do not need to wait for him to leave to shimmy down the pole. You can drop from beam to beam until you reach the bottom of the shaft. While hanging from the top, drop, then catch the next ledge/beam. This will take you to the garage where your extraction point is located.