- The Citizen 2 opening cinematic has been improved.
- Subtitles added.
- Dr. Lambs can now heal the player.
- Shotgun Combines now have their own model from Half-Life 2: Episode Two.
- Music now plays during Larry's capture in the stadium battle and when Larry makes his television appearance.
- Added a wooden car model to the playground.
- The design of some rooms has been changed (for example, the attic from which the player needs to send a dove).
- New dialogues have been added.
- Added Alliance satellite dish.
- Added a model of the first aid kit that needs to be brought to a wounded rebel.
- Dr. Brin's propaganda speech can now be heard in many places.
- The voice acting has become more varied.
Chapter 1-2: A Way Out
The Citizen and Larry arrive at a subway station and exit onto the street. According to Larry, there aren't many Combines in the area they're in. They enter a house together and encounter a force field. The Citizen needs to disable it to proceed. He disables it, saving a girl from the Civil Defense. Crossing to another street, they witness a man being killed by a sniper. The Citizen quickly eliminates him, but is immediately met with fire from a second sniper, whom he also eliminates.
The heroes continue on their way, avoiding a series of mines. Larry, who knows the local channels, shows the Citizen the way. Having reached their destination, the heroes disembark and enter the station. Meanwhile, Combine forces attack the station, forcing the heroes to defend themselves. After fighting them off, Larry and the Citizen finally reach the rebel base. Here, they find Sarah, a familiar character from previous installments. Together, they continue on.
Chapter 3: The Missing Gear
Larry plans to conduct a special operation against the Alliance, using the station's safehouse as a staging area. He plans to overload the core by blowing up the factory where "Dr. Breen's Personal Reserves" are produced. He plans to access it through an old shaft located beneath the factory. Once assembled, everyone boards the boat, and the Citizen returns to pilot the airboat.
Chapter 4: Sailing Along
The Citizen's job is to protect the boat. Upon reaching their destination, the rebels disembark and enter the hangar, where they discover a Myrmidon. It attacks one of the soldiers, but the soldier reacts and jumps back, causing the Myrmidon to crash into the door, knocking it down. After defeating it, the rebels discover a room behind the broken door, set up by the Alliance for their own use. The Citizen is taken down in an elevator.
Chapter 5: It Makes You Forget
Once in the shaft, the Citizen looks around. Larry follows, followed by Sarah and everyone else. They then turn on the power and, looking at the monitor, notice a squad of Combine heading their way. They meet it and destroy it. They then climb the stairs, and the citizen must open another door. Separating from the squad, the citizen enters the factory by a different route. Here, he encounters resistance from the combine harvesters. Having defeated them, the citizen continues his triumphant march.
Chapter 6: Manual Override
Having dealt with the plant's security, the citizen meets his comrades. Larry breaks the glass and climbs up the cable, aiming to raise the elevator. Left alone with the citizen, Sarah tries to strike up a conversation. She explains that they lost several men while infiltrating the plant. Finally, the elevator begins to ascend, with Sarah and the citizen on the roof. Reaching the panel, Sarah attempts to activate the self-destruct. It turns out the only effective method is to manually press the button a second before the explosion, which will destroy the core and the entire plant, as well as kill anyone remaining.
Ending: Stay
Seconds before the explosion, Larry presses the right button, and both die. Their photos end up on a stand with all the dead rebels, which Sarah looks at. Interestingly, there is no photo of the Citizen as such—we never get to see him from the outside. The photo depicts a dark silhouette with a smiley face and a question mark. The credits roll.
Ending: Leave
The Citizen leaves with Sarah. They descend into the mines, open the door, board the mine carts, and ride away. The blast wave overtakes them, but they manage to survive. The heroes reach the coast, where they are met by surviving rebels. The boat on which the detachment arrived arrives. The radio reports that Gordon Freeman has broken through to the Citadel. The credits roll.