The Black Mesa Research Facility is an ultra-secret laboratory under a government contract to conduct top-secret and extremely volatile experiments. The scientist Gordon Freeman is a Black Mesa employee. One morning, as usual, he pits his way to the research facility for a run-of-the-mill experiment. However, Gordon comes to realize that it might not be as ordinary as he thought. Odd things happen as he makes his way to one of the Black Mesa test chambers. Even stranger things happen when he begins to move the test sample towards the anti-mass spectrometer.

At that moment, everything goes horribly wrong. Aliens from the dimension Xen suddenly invade the facility, injuring or killing many of the employees. Soon afterwards, marines arrive to contain the situation by killing the aliens as well as the surviving human witnesses. Gordon understands what that means: he will have to fight his way through both aliens and marines to get to the top of the Black Mesa complex and to freedom.