Once open, 4 areas will become available for changes: Controls, Video, Audio, and Game. Open your inventory and drag the Sympathetic Resonator onto the shield generator. This is a really free-form level, so there's many different ways to go about clearing it.
Check out Tom's System Shock 2 reinstall for a sense of why it was so important, and why it's still worth playing. Go through the room with the Xerxes mainframe, then go to the two-leveled room with the Bio-Reconstructor, from there, take the door on the lower level, the right door in the next room, jump through the glass onto the upper level, then down the short hall.
The Climax Boss is the boss at a pivotal moment of the story.
