You are still trapped in the derailed train. To escape, simply walk down the train carriages until you reach the door. Alyx will find you and remove the door with the gravity gun, then give it to you. Head out to the right, and open the door with the gravity gun.
Alyx will take a look at the Citadel, trying to figure out what is happening when a portal storm creates a shockwave that destroys the bridge and takes out a wire fence blocking a path into the mine.
The mine is partially blocked by obstacles. The first one is minor, which can be ducked under (unless it is destroyed), and the second one requires you to smash the bench with the gravity gun then crouch under it.
The mine has a few zombies, where you can hit them with objects that you can pick-up. Alyx will also attack them as necessary. Zombies and antlions are fighting outside, and they can be taken out with a simple gas canister.
Enter the building, and Alyx will try to get the communication array to link up with her father. Since something is wrong, Alyx will try to see what's going wrong with the system, but it's as simple as plugging a cord into the socket. After the discussion with Eli, the combine will interfere with the transmission; exit via the newly opened door.
The exit leads to a small mine tunnel that has a blocked entrance. At the top of the tracks is a cart loaded with heavy weights - shoot the wood beams near the cart with the gravity gun to smash the blockade.
You should now be outside a small mining town. To enter, take the right path.
You need to open a gate that's blocking the path. Look for a ladder in the far-right corner, and climb it. You will enter the building from the roof, and press a button to raise the gate. Exit by the trapdoor, go through the gate(s) to the right, and head to the mine.
To activate the elevator, take the crowbar with the gravity gun.
Advance into the mines. You first have to use the elevator to go over the chain-link fence, and go from above. The antlion you see will flee on sight. Go down the tunnel, and down a few stories, until you see a head crab; kill it.
Go down the hole. You will go through a small antlion tunnel, with grubs on the walls. This short tunnel ends in a small mine section. From there, you will see an acid antlion, which will attack. There are two more acid antlions as well. Within this area, collect the magnum and shotgun - you will need them. Go into the hole within the weapon area, and climb out behind the fencing. Remove the obstruction and proceed back into antlion terrotory.
Go up the ramp to the right, defending yourself from other acid antlions. After going up, jump onto the rocky platform, and into the water. At the other end of the tunnel, you should see some ammunition, as well as nearby barnicles and distant antlions fighting. Proceed onward.
When it appears that you are entering a branching passage, you may see a few acid antlions. Kill them. The map exit is behind an antlion web, and starts the next chapter.