However, during the experiment something does not go as planned and Freeman unintentionally opens an interdimensional hole that gives access to a parallel world called Xen, which is populated by extraterrestrial creatures (the best known are the vortigaunts or "slaves"). During the incident the test room where Freeman was was destroyed by the sequence of resonances, but he manages to escape from there thanks to the protective suit. After returning to his dimension, having been caught in a storm of portals, he will have to deal with the unintended consequences of the experiment upon discovering that a horde of aliens has invaded the scientific complex, attacking its staff and destroying everything in its path.

As he moves around the place, Gordon will find in his path human corpses, debris and voracious creatures chasing the survivors. Our protagonist, with the support of casual colleagues and security guards from the center, will confront the aliens in order to survive and return to the surface, to seek help. Freeman's talent will allow him to exploit a vast arsenal and stay alive while trying to understand what happened. During your trip, you discover that the U.S. government is trying to cover up the accident by sending a special elite commando to hostile environments. Numerous well-equipped soldiers will enter the wreckage of the underground complex in order to contain the alien invasion and silence the surviving Black Mesa personnel. No longer expecting help from the outside, Freeman, with the advice of his fellow survivors,sets a new goal: to try to reach the Lambda complex on the other side of the Black Mesa facility, where there is a path to Xen with which to end the alien invasion.

As he progresses, Gordon will face increasingly difficult, dark and strange situations. Among the mysteries that surround him, there are the appearances of a strange character who watches Gordon from a distance and who appears to be a man dressed in a blue suit carrying a dark briefcase. The role of this mysterious character known as G-Man, will not be revealed at any time. Eventually Freeman is teleported to Xen, where he discovers that he is not the only one who has reached the place as he will find corpses sheathed in special suits like his that previously tried to confront Nihilanth, a being of Xen who keeps the portals to Earth open. However, unlike his predecessors, Gordon succeeds in destroying the gigantic creature thus ending the threat of the portal. Or so he thinks.

After the feat, G-Man will make an appearance capturing Gordon and placing him in an automated monorail like the one that transported him at the beginning of the story, while telling him: "... I took the liberty of stripped him of all his weapons, in any case, most were owned by the government. As for the suit, he earned it...'

Finally G-Man proposes to Gordon to work for his "employers" with "an offer that he will not be able to refuse". From that point on, there are two possible endings to the game. If Gordon accepts the proposal, then G-man will put him in "hibernation" mode for an indefinite time until it is of use to him. If gordon decides instead to refuse the offer, then G-Man teleports our protagonist to an unknown place where he will appear devoid of weapons and surrounded by hostile aliens approaching him, implying that Gordon dies...