Use the walkways you create to reach a switch inside a small glass enclosure within the room. Use the energy balls to take out the stalkers on platforms across the room, then activate the energy bridges via the receivers in the room (one's directly overhead). Before you do anything else, use the gravity gun to grab energy balls from the tall beam to the right. The platform will take you to a large room with the unstable core. Follow Alyx around a bit and she'll lead you to an elevator you must take on your own.
Lead Alyx through the next doorway and be ready to take on a few Combine soldiers.
