Your unit, Epsilon team, is made up on ex-Black Mesa personnel forced to work for the Administrator's employers (henceforth known as the Organisation) after the Incident, during which Xen came under the Organisation's control. Recently, though, difficulties have been created for the Organisation by alien rebels attempting to liberate Xen, as well as the US government, with whom the Organisation is not directly associated.

Government forces had recently recovered a crystal of immense power -- the ownership of which could permanently consolidate the Organisation's hold on Xen. The Xen rebels had also learnt of its existence, however, and planned a major assault on the compound in which it was held.

Your team has been instructed (partly by one of the Administrator's lackeys, the alien clone named Tor) to retrieve the crystal in the resulting confusion. Due to some computational error or malfunction, you found yourself far from the intended insertion point, slap in the middle of the military-rebel conflict. 

Worse still, your entire team has been led into some type of aquatic trap by Barnabus the security guard. Your lungs strain for air, the genuine floating sensation intensifies to the point of absurdity, and your vision becomes shaded by ever-darkening void.