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A Nova Prospekt Reunion
Step out toward the railroad track and watch Alyx take out a Combine. Drop down and start walking forward under the tracks. Alyx will stop you at gunpoint for a brief second, then join up with you. For the time being, you just need to follow Alyx. She'll open the elevator door with her electrical device. Step inside and ride it to the top. Three soldiers come out from the sides when the door opens. Help Alyx kill them, then follow her into the security room. She'll check the panel and then tell you to head out again.
Go down the hallway toward the stairs. Three soldiers come down them as you approach. The shotgun will make short work of them. Then go up the stairs into the hallway up here. Four Combine are around the two sides. Take them out with the shotgun or the SMG and follow Alyx into the room with her father. Leave with her once the reunion is over.
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Some Alone Time
You're on your own for the time being. Go through the door and open the side door. Kill the two fast headcrabs and break open the supply crates in back. Go back out and clear a path down the little hallway to the door. Step inside and just wait for a second until Alyx opens the door. Walk down the main hallway to the next cell door. It's jammed, so Alyx will send you to the office. Knock over the cabinets with the gravity gun and go into the vent behind them. Get out your crowbar now. There are three normal headcrabs in the vent and you have to kill them. Knock the grate off at the end with the gravity gun. With any luck, it will set off the laser tripwire. If it doesn't, then you'll have to pull a barrel over to set it off. There are four fast headcrabs here too. Kill any of the survivors from the safety of the vent.
Drop down once it's safe. Look to the double doors at the end and notice the cracked window. Arc a grenade through the hole and try to knock over those turrets now. That will make things a bit easier later on. Alyx will open the cell door in a moment, so go through it.
Go into the office and Alyx will warn you of a large group of soldiers moving toward you through the other jail cell. There's an infinite box of grenades in the office. Grab some and start throwing them out toward the door through the holes in the window. Six Combine will work their way into the room. It's dark, so look for their yellow eye wear to spot them. Once they are dead, chuck a grenade down the hall they came down. That will knock over the two turrets at the end.
Go through the hallway and turn the corner with shotgun in hand. It's perfect for this range. Blast the one guard behind the low shield. Then round the corner and shoot the two soldiers right by the door. Another will come out of the little office. Shoot him too. That force field is plugged into the little office, but you can't get a line of sight on it with your gravity gun. Go to the farthest edge and look into the office. You should be able to toss a grenade into the room. The explosion will knock the plug loose and let you through.
Round the corner and keep your gravity gun out. There's a turret in the little niche, so pick it up and toss it away. Round the corner again. If you took out those turrets earlier by throwing the grenade through the window, then you can just walk past. If you didn't, then the turrets will still be standing. Crouch behind the barrels and pick one up for a shield. Then just move to the side and duck into the side room. Go through until you hit a loading screen.
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The First Turret Battle
Go into the control room and kill the two soldiers inside. Heal up at the health terminal, then press the little red button on the turret storage cabinet. Pick up a turret and put it on the edge of the little platform by the staircase. Make sure it can aim down at the floor. Repeat the process for the other side. Once they are set, the Combine will start coming through the force fields on the ground level. The turrets should be able to handle most of the soldiers by themselves. Just stay in the control room and keep an eye on them. The only real danger is that a grenade or a man hack might knock them over. Soldiers will also make it past them and knock the turret over with a melee attack. Just stay calm and kill the threat. Then pick up the turret with the gravity gun and set it back up. After about four waves, Alyx will drop down through the vent above you and the attacks will stop.
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A Shocking Time in Nova Prospekt
There's a little scene where you learn Mossman's true loyalties. They certainly didn't foreshadow that by making her an obvious turncoat in chapter 5. Regardless, Alyx will kill the force fields below. Drop down and go down the corridor on the left.
Round the corner and clear a path to the door. Go down the steps and get a good look at the electrified water. If you step into it, you will take a whole lot of damage fast. So...don't step into it. Jump over the railing and onto the pipe. Step out and jump onto the blue barrel in the water. Then jump onto a wooden pallet. Use your gravity gun to drag those boxes over. Two headcrabs might attack. Just punt them into the water with the gravity gun to kill them. Go along the boxes until you can jump onto the stairs. Go up and grab the barrels on the upper level. Use these to form a bridge to the other ledge. Kill the last headcrab on the other side and go through. Go up the stairs and go through the only intact door. There's one zombie in the room with the electrical panel. Another three zombies come through the side door. Kill them with the shotgun. Go through the only exit and reach the area above another prison block. Kill the few soldiers below you before jumping over the rail.