Use the Spectre to get to the entrance, but make sure the Spectre is not destroyed. Continue through the level as you would normally from that point on. Then, when you reach the part where Johnson takes control of the Scarab, just do what you would do if you were going to try to land on it to get inside. If you do not know how to do this, see How To Get Inside the Scarab in The Great Journey.
After you are on board, push Johnson to the edge of the Scarab. Then push him over, so he falls down onto the sand below the Scarab. After that, jump from the main gun on the Scarab, back onto the platform with the Brutes. When you jump, it is best to activate your Active Camo. Do not kill the Brutes on the platform when you jump on it. Go back through the complex, retracing your steps. Get back to the ground where you left the Spectre, and find where Johnson has fallen from the Scarab. Go to where he is, and back up the Spectre, so that the back is in front of him. He will enter the turret seat.
Now here is the tricky part. There is a mound of rocks next to the platform up above, with the Brutes still on it. Using the air brake and speed boost on the Spectre, raise the nose of it and boost up the wall of the mound. When on top, Sgt. Johnson will be able to shoot the Brutes from there with the turret. When all the Brutes are dead, a cutscene will trigger (Backseat Driver). Now drive the Spectre with Johnson in the back all the way to the Control Room. Go underwater until you reach a ramp-like wall of rock. You do not need to air brake or speed boost up this one. Just drive up, until you are above water and on the Control Room island. Drive up the island, until you reach the Control Room exterior. Now continue forward, then when you get to the ramp that leads to the door to enter the Control Room, go up the ramp. Wait for the Scarab to blow up the door, now drop down in front of it. Guide the Spectre through the rubble of the destroyed door. After some hard work and good driving, you will be able to drive through into the room with the Brutes. Drive past them to trigger the cutscene.
You will now be in the Control Room. Go behind you, and do as you would if you had taken a Banshee with you. Go into the corridor before the Control Room, and there will be your Spectre, with Johnson still inside it. Drive the Spectre into the Control Room. Drive over the platform onto the area where you fight Tartarus. You may need to use one of the rotating platforms around the outside to help you. Land on the part where you fight Tartarus, and reverse the Spectre so the back (where the turret and Johnson are) is directly in front of one of the holes that lead to the bottom floor. If you fall onto the bottom floor and crouch, you die, because the floor is too low and too close to the death zone. Johnson always crouches when he lands after a jump. So, get out of the Spectre, and go to the side of the turret. Press X to get in the turret. If you positioned the Spectre correctly, Johnson will get out for you, so you can go in the turret, but he will fall down to the bottom floor. Because he crouches when he lands, he will die as soon as he hits the ground.