Eventually, the player fights through the facility and teleports to Xen to try to seal the tear from the other end, where a Xen creature is keeping it open. This serves to foreshadow many of the challenges the player will face, as well as the labyrinth-like structure of the game. In Half-Life, protagonist Gordon Freeman is introduced to the facility in a notable sequence involving very little interactivity. The resulting crisis is seen from several points of view in Half-Life and its expansions.

There are many notable creatures that come from Xen, such as the Vortigaunts and Headcrabs. As a result, Xen creatures are teleported into the facility and prey on its human inhabitants. At the beginning of Half-Life, one such crystal, revealed in Half-Life 2: Episode Two to have been provided by the G-Man, is put through an anti-mass spectrometer and causes a resonance cascade, tearing the spacetime continuum. Creatures and crystals from Xen are subsequently brought back to the facility for testing. Prior to the beginning of Half-Life, scientists experimenting on teleportation discover Xen, a border dimension somehow intrinsically involved in the teleportation process.

Over the course of the series, Black Mesa is revealed to be conducting top-secret research into various fields, such as teleportation and experimental weapons research.

This facility is depicted as a vast series of underground research laboratories as well as surface constructions such as offices, chemical waste disposal plants, and personnel dormitories (even cafeterias, where Gordon Freeman can destroy Doctor Magnusson's microwave casserole), all powered by a hydroelectric dam and connected by an advanced tram system. The base is a decommissioned ICBM launch complex at an undisclosed New Mexico desert location, which has been converted into a scientific research facility and bears a number of similarities to Los Alamos National Laboratory, Sandia National Laboratories and Area 51. The Black Mesa Research Facility (shortened to B.M.R.F) is the primary setting for Half-Life and its three expansions: Opposing Force, Blue Shift, and Decay.

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