To your right is the start of a large spiral staircase. Go down to the first door on the right, open it, and go through. Ha'rar is somewhere inside, but you won't be able to save him. Sit in the chamber overlook (up the stairs) and watch the enforcers kill the poor scientist while cursing the injustices of Pfhor society. Go back outside, and kill anything you see.
Going down the stairway, you will pass several rooms. One of these is a control tower overlooking a juggernaut bay, the next is a computer room with a terminal that slides down from above and much ammunition, and the last is a lower control level overlooking the same juggernaut bay you saw earlier. In all of these rooms, kill anything you see, except for the juggernauts, because you won't be able to reach them, and the S'pht'Kr, because they're on your side.
At the bottom of the stairs, you'll enter the central shaft. Go through one of the two blue air seal gates, read the terminal, and use the pattern buffer. Proceed into the elevator, and push the button closest to the terminal. (You won't be able to go through the big double door on the upper level.) At the bottom, open the large double door by pushing the button nearest the door. Kill anything you see, or at least try to.
In the middle of the large corridor the elevator opens on, you'll find two sets of stairs. You don't need to go to the upper hallway. Go to the lower hallway. Open the first door at the bottom of the corridor, and go through to the second door. Through that door is the engine overlook room. There are two sets of circuits on either side of the room, which will open automatically when you near them. Destroy all four circuits, and return up the stairs, the elevator, and the spiral stairs back to the room with the terminal hanging down from above. Use this terminal to teleport out.
In the overlook room of the execution chamber, there is a secret door in the wall. Inside you will find an elevator going down to the bottom of the spiral stair; at the bottom is an invincibility powerup. If you arrange things carefully, you can grab this, run through here, grab the powerup, and jump down into the big battle at the bottom with enough time for the invincibility to help you.