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The Second Turret Battle
It's time for the second turret battle. The difficulty is really amped up though. I personally consider this the hardest one.
More soldiers are coming, but they won't spawn before you set the third turret down. You don't have to rush. Go ahead and use both chargers on the wall. Press the two buttons to unlock the three turrets. You shouldn't set up here though. If you set the turrets up at the door, then the soldiers passing through the forcefield will be so close that they will constantly knock the turrets over. Set up in the other room with the ammo box. It's roughly in the middle, so you are in a better strategic position. Put two up on one side and one on the other. Take up a position in the center with a shotgun and kill any soldiers that get too close. If they manage to knock one over, then set it back up.
You will need to last through a fairly steady wave for about four minutes. Alyx will eventually mention a “mother lode" of soldiers coming. They'll make one last push with double the soldiers and man hacks. Survive it and Alyx will join with you again. Follow her out of the newly opened cell door and charge up at the two new chargers. Then go through the door.
As a side note, if you can't make a stand at the ammo box, then there is another area that's easy to defend. It's also very boring. If you are being overrun at the ammo box, then grab a turret and run into the lit prison cell by the room with the ammo box. Set the turret at the door and get back in the cell. The turret will be very hard to knock over because it's supported by you and the door frame. If it is knocked over, you can quickly set it back up. Their only angle of attack is covered by the turret too, so you can just sit back and blow away the occasional man hack or soldier who gets too close.
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Go down the steps and into the hallway. The Combine will turn off the lights and just throw a bunch of flares. Split off to the right and start shooting. Use the AR2 and some grenades to blow them away. The grenade launcher on the submachine gun should come in handy for this part. Once they are dead, go through the door they were guarding.
There isn't any more combat for a few minutes. Just follow Alyx around as she talks to Mossman. When you go into the teleportation room, walk by the turrets and use the chargers on the walls to heal up before the last fight.
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Third Turret Battle
This is actually a lot easier than the second one. You can't do anything until after Mossman betrays you, so just wait. Alyx will eventually unlock the turrets. There are three main points of access into the room. The door by the turrets is sealed and will not open. You need to just cover the three other sides.
Put one turret on the glass section of the floor and have it face away from the entrance and toward the opening through the glass doors. Take another and place it on the right side of the teleporter facing the forcefield. Put it between the console and the stairs. Place the final one by the teleporter and have it face to the left access point. It should be right in line with the one on the glass floor, but make sure it is behind the rail.
Now you just have to hold until the teleporter resets. You can watch the elevator inside the teleporter to monitor your progress. The right side never comes under heavy attack, so that turret should be fine. The one by the rail is propped up well, so it's not at risk. The only one in real danger is the one on the glass floor. Keep an eye on it. Alyx is effectively a mobile turret, so you have plenty of firepower. Just use the AR2 to pick off anyone that gets too close, and wait it out. Jump into the teleporter once Alyx tells you to do so.
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Dr. Kleiner's Lab
You'll come out a week later in Dr. Kleiner's lab. Get the status update from him and just wait for a minute. Alyx will stay behind to escort Kleiner, but you get to leave with Dog. Go out to the main hallway and drop down the shaft to start the next chapter.