After defeating the Hunter Chopper, Gordon drives his airboat off a nearby dam and into the river below. He finds himself in front of Black Mesa East, a power station which, if not for the telltale Lambda symbol sprayed nearby, would seem completely innocuous.
Disembarking from his airboat and venturing inside, Gordon enters an airlock. The doors shut behind him and some scanning equipment comes to life as a voice on a intercom reassures him he's safe. Said voice is that of Dr. Judith Mossman, who introduces herself as a longtime admirer of the work Gordon did with Eli and Kleiner prior to the Black Mesa Incident. As the airlock opens up, she escorts Gordon down to Eli's lab while explaining to him the developments the Resistance had made regarding teleportation.
Gordon and Mossman enter the lab, where Eli and a Vortigaunt are working on fixing his teleporter device. Eli greets Gordon warmly and reminisces about the how he last saw him just after the Resonance Cascade. Mossman excuses herself to do some work in the adjacent room, at which point Eli tells Gordon he's free to look around the lab.
Depending on what he examines, Eli will have certain information to dispense:
- If Gordon looks at the board of newspaper clippings, Eli brings up the Seven Hour War and how Dr. Breen ended it by negotiating with the Combine, and became administrator of Earth in exchange.
- If Gordon examines Eli's family photo, Eli asks if he remembers his wife Azian, then laments on how said photo and Alyx were the only things he managed to rescue from Black Mesa.
- If he examines a strange jar containing what looks like a head, Eli claims Alyx brought it in but that he still has no idea what it is.
- If he looks at the teleporter, Eli remarks that the teleportation relay between Kleiner's lab and his is nearly fixed, but they have no idea what went wrong in the first place.
A short while later, Alyx enters the lab, visibly shocked that Gordon got there before her but nonetheless glad he's safe. She gets to work on maintaining the teleporter, but then Mossman comes back from her own duties and she and Alyx start fixing to argue with each other. Eli breaks the tension by suggesting that Alyx should take Gordon outside and teach him how to use the Gravity Gun, which she obliges.
Gordon accompanies Alyx as the two of them head to the scrap yard out back. On the way they pass a sealed-off door, which according to Alyx leads to Ravenholm, a place that nobody goes to anymore. Out in the scrap yard, Alyx helps Gordon become acquainted with the Gravity Gun, a tool originally made for clearing minefields that also comes in handy for carrying and throwing large objects. Once Gordon is familiar with how it works, Alyx introduces him to D0g, her hulking robot companion, and gets the two to play catch with each other — D0g uses his in-built Gravity Gun to hurl crates at Gordon, who catches them with his own.
Their playtime gets cut short, however, by an all-out Combine attack on the base. Alyx, Gordon, and D0g head inside to try and regroup with Eli, but Alyx is cut off from the other two by falling rubble. She tells D0g to take Gordon to the Ravenholm passage and try to circle back, then heads off to look for her father.
D0g escorts Gordon to the Ravenholm passage and holds the door open for him, then shuts it and runs off. Gordon ventures further into the passage on his own, but doesn't end up finding a way to circle back to the lab and instead finds himself at the doorstep of a long-lost town...
This chapter contains examples of:
- All Your Base Are Belong to Us: The Combine launch an assault on Black Mesa East not long after Gordon arrives.
- Call-Back: The faceplate of a HEV charger from the original Half-Life can be found in the scrap yard.
- Developer's Foresight: After obtaining the gravity gun, if the player pulls the barrel down before Alyx says to try pulling them down, she skips the mention of the barrels and instead says "Try pulling something towards you".
- Involuntary Group Split: Happens at the end, when the Combine shells the hideout and causes a cave-in. Alyx is separated from Gordon and D0g by falling rubble during the Combine attack.
- Justified Tutorial: The Gravity Gun and its functions are organically explained through Alyx teaching Gordon how to use it.
- Newspaper Backstory: The newspaper clippings in Eli's lab provide insight as to what happened between the first game and this one, namely the portal storms and the Seven Hour War.
- Precious Photo: Eli keeps one of his family in his lab.
