At the underground Black Mesa Research Facility, physicist Gordon Freeman participates in an experiment on a crystal of unknown origin. This triggers a resonance cascade, which causes widespread damage and teleports in hostile alien creatures. Venturing to the surface, Freeman discovers government soldiers have been dispatched to cover up the incident by killing humans and aliens alike. He is instructed by a scientist to make his way to the Lambda Complex to stop the alien invasion.

Freeman kills a giant creature inside a rocket engine test facility. He uses an underground monorail to reach a rocket silo, where he launches a satellite to help the Lambda team. Freeman is captured by soldiers and left for dead inside a trash compactor. Escaping through a waste treatment complex, he discovers a laboratory filled with alien specimens, collected long before the resonance cascade.

Overpowered by the aliens, the soldiers begin to withdraw. Freeman fights across a military base to reach the Lambda Complex, where he discovers secret teleportation technology. There, scientists inform him that a powerful alien creature is preventing them from closing the portal. They teleport him to the alien dimension of Xen to kill it.

Freeman encounters dead scientists who teleported there before him. He kills a large alien, the Gonarch, and finds a factory that manufactures alien soldiers. Finally, he discovers the Nihilanth's lair and kills it. Freeman is detained by the G-Man, a mysterious interdimensional agent who claims his "employers" wish to hire him. If he accepts, Freeman is placed into stasis; if not, he is teleported to his death.

Earth has been conquered by the alien Combine, who have implemented a brutal police state. In City 17, Alyx Vance (Ozioma Akagha) and her father Eli (James Moses Black) are arrested by Combine forces as part of a crackdown on the Resistance. The Resistance member Russell (Rhys Darby), an inventor, rescues Alyx and warns her that the Combine are planning to transport Eli to Nova Prospekt for interrogation.

In the quarantine zone, an area of City 17 overrun with alien creatures, Alyx meets a vortigaunt named Gary (Tony Todd). He asks her to save his fellow vortigaunts and foresees that Eli will die. Alyx derails the train carrying Eli, who is rescued from the wreckage by Gary. While in custody, Eli learned that the Combine are storing a superweapon in a vault inside the quarantine zone. He instructs Alyx to find the vault and retrieve its contents.

Alyx fights past Combine forces and shuts down a power station keeping the vault aloft. She discovers that each station is powered by an enslaved vortigaunt. She rescues the station's vortigaunt, who promises that the vortigaunts will disable the remaining stations. Alyx moves through a distillery, where she escapes a hazardous waste worker, Jeff, who has succumbed to alien infection. Eli contacts Alyx and warns her that the vault is a prison built to contain something discovered by the Combine. Russell reasons that it holds Gordon Freeman, and Alyx crashes the vault to the ground. Instead of finding Freeman inside, she releases the G-Man.

As a reward for freeing him, the G-Man offers his services to Alyx. She demands the removal of the Combine from Earth, but the G-Man says this would not be in the interests of his "employers". He instead shows her a vision taking place five years in the future, and offers her the chance to change the outcome of Eli's death at the hands of a Combine Advisor at the White Forest rocket facility. Alyx complies, killing the Advisor and saving her father. The G-Man informs Alyx that she has proven herself capable of replacing Freeman, with whom he has grown dissatisfied. Despite Alyx's protests, he suspends her in stasis and leaves. Five years later, Freeman regains consciousness at White Forest and is reunited with Eli. Realizing that the G-Man has Alyx, Eli declares his intention to kill him and hands Freeman his crowbar.

After the alien invasion at the Black Mesa Research Facility, a multidimensional alien empire known as the Combine has conquered Earth. Approximately twenty years after being placed in stasis, Gordon Freeman is inserted into a train bound for City 17 by the G-Man (Michael Shapiro). Helped by the undercover Resistance member Barney Calhoun (Shapiro), Gordon attempts to reach the laboratory of Dr. Isaac Kleiner (Harry S. Robins) but is subdued by Combine officers. He is rescued by Alyx Vance (Merle Dandridge), who guides him to the laboratory. Kleiner's attempt to teleport Gordon to the Resistance base fails, and Gordon is momentarily teleported to the Citadel, the skyscraper headquarters of Dr. Wallace Breen (Robert Culp), the former Black Mesa administrator and the Combine's puppet ruler. Gordon progresses to the base using the city's canal system using an airboat, eluding Combine forces.

At the base, Gordon reunites with Alyx's father, Dr. Eli Vance (Robert Guillaume), and meets Dr. Judith Mossman (Michelle Forbes). Alyx introduces Gordon to her pet robot, Dog, and gives Gordon the gravity gun. Combine forces storm the base and capture Eli and Mossman. Gordon diverts through the zombie-infested town of Ravenholm, aided by its lone inhabitant, Father Grigori (Jim French), to a Resistance outpost whose occupants provide him with a dune buggy. He drives along the coastline of depleted water levels to reach the Combine prison of Nova Prospekt, where Eli and Mossman are being held. Gordon and Alyx reunite, locate Eli, and discover that Mossman is a Combine spy. Before they can stop her, Mossman teleports herself and Eli to the Citadel. The teleporter explodes moments after Gordon and Alyx use it to escape Nova Prospekt.

Returning to Kleiner's lab, Gordon and Alyx learn that the teleporter malfunctioned and that a week has passed, during which time the Resistance has used the attack on Nova Prospekt to launch an armed rebellion against the Combine. Aided by Barney and Dog, Gordon fights his way to the Citadel. Inside, a security system vaporizes his weapons but inadvertently super-charges the gravity gun; this helps Gordon climb the tower. He is captured and taken in a transport pod to Breen's private office, near the Citadel's apex, where he and Mossman are waiting with Eli and Alyx as captives. Breen reveals that he plans to use them as leverage to negotiate with the Combine, contradicting what he had told Mossman. Angered, Mossman frees the captives and Breen attempts to escape using a teleporter. Gordon destroys the reactor and Breen falls into the abyss. Moments after the reactor explodes, the G-Man reappears and freezes time, praises Gordon's actions, and returns him to stasis.

In City 17, Gordon Freeman and Alyx Vance (Merle Dandridge) have destroyed the Citadel's reactor. As it explodes, several vortigaunts (Louis Gossett Jr.) appear and extract Alyx. The G-Man (Michael Shapiro), who extracted Gordon from the explosion, is confronted by the vortigaunts and his psychic connection to Gordon is severed.

Gordon awakens in the ruins of City 17, where he is rescued from a pile of rubble by Dog and reunited with Alyx. Alyx makes contact with Dr. Eli Vance (Robert Guillaume) and Dr. Isaac Kleiner (Harry S. Robins), who have escaped the city. Kleiner informs them that the Citadel's core will soon collapse and destroy the city.

Gordon and Alyx proceed into the core to temporarily stabilize it. Alyx discovers that the Combine is attempting to accelerate its destruction to send a transmission back to their homeworld. She downloads a copy of the transmission and a video recorded by Judith Mossman (Michelle Forbes), in which she discusses the location of an unknown project before being subdued by a Combine attack.

Gordon and Alyx board a Combine train to escape the Citadel, but it derails. They proceed underground and through the city streets, fighting past disorganized Combine forces and rampant Xen wildlife. Near a Combine-held train station, Gordon and Alyx reunite with Barney Calhoun (Michael Shapiro), to evacuate refugees from the city. They escort the refugees and take a different train out of City 17, escaping just as the reactor detonates, which delivers the Combine transmission. As several pods containing Advisors flee the collapsing Citadel, the explosion's shockwave derails the train.

The Combine have opened an interdimensional portal in place of the destroyed Citadel, to summon reinforcements and defeat the Resistance. Outside City 17, Gordon Freeman and Alyx Vance (Merle Dandridge) escape the wreckage of a train they used to flee the city. The two proceed to a transmission station, where they make contact with Dr. Isaac Kleiner (Harry S. Robins) and Dr. Eli Vance (Robert Guillaume), who have arrived at the White Forest rocket facility. Kleiner and Eli learn that a copied Combine transmission Alyx is carrying may be able to close the portal. The pair reach an abandoned mine, where Alyx is critically wounded by a Combine Hunter. A vortigaunt (Tony Todd) leads the two to an underground outpost, where Gordon is instructed to help gather larvae from a nearby antlion colony to heal Alyx. After the larvae are gathered, vortigaunts begin to heal Alyx. With their abilities diverted, the G-Man (Michael Shapiro) can now connect to Gordon. He reveals that he rescued Alyx from the Black Mesa Incident despite objections from an unspecified third party, and it is imperative she reaches White Forest. The G-Man instructs an unconscious Alyx to tell Eli to "prepare for unforeseen consequences".

After Alyx recovers, they reunite with Eli, Kleiner and Dog at White Forest and are introduced to Dr. Arne Magnusson (John Aylward). The scientists are preparing a rocket which they plan to use with the code to reverse the portal. After Gordon subdues a Combine attack on the facility, Alyx gives Kleiner a message recorded by Judith Mossman (Michelle Forbes), which contains the location of the Borealis, a vanished Aperture Science research vessel. Kleiner believes the vessel contains technology capable of combating the Combine, but Eli argues the vessel should be destroyed. Both agree that Alyx and Gordon should travel to the ship and locate Mossman. Alyx unconsciously delivers the G-Man's message to her father, troubling him. Gordon learns from Eli that the G-Man provided the test sample which caused the Black Mesa Incident, warning Eli with the same message as Gordon entered the test chamber. He promises to explain more after the portal is closed.

While the scientists prepare the launch, White Forest is under another Combine attack. Gordon defeats the attackers using explosive weaponry created by Magnusson. The scientists launch the rocket and close the portal, trapping all remaining Combine forces on Earth. As Alyx and Freeman prepare to leave for the Borealis, Eli warns to Gordon about the ship's "cargo". The trio head to a hangar to board a helicopter, but two Combine Advisors suddenly appear and restrain them. Eli is killed by an Advisor before Dog can chase the Advisors away. Alyx, sobbing, clutches her father's body