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Gina Cross and Colette Green arriving at the Anomalous Materials Labs at Black Mesa and reporting to Dr. Keller, who is readying the day's analysis of an unknown specimen. Despite the objections of Dr. Rosenberg to pushing the analysis equipment beyond its design capacities, Cross and Green are assigned to assist setting up the experiment for Gordon Freeman. When Freeman inserts the specimen into the scanning beam, however, it triggers a "resonance cascade", causing massive damage to the facility and teleporting alien creatures into the base. Keller and Rosenberg agree that Black Mesa cannot deal with the situation on its own, and so decide to call for military assistance. Cross and Green escort Rosenberg to the surface, where he sends a distress signal to the military. However, the military are ordered not only to contain the situation, but to silence the base by killing its employees. Rosenberg elects to stay behind to meet with the military on arrival and Cross and Green return to Keller.
Once reunited with Keller, Cross and Green work to seal the dimensional tear to stop the invasion. The military arrive and try to remove all personnel as well as the alien force. After resetting key equipment to prevent a second dimensional rift, the two are tasked with preparing a satellite for launch. The satellite, which is launched by Freeman in Half-Life, is used in tandem with ground-based equipment to significantly weaken the effects of the resonance cascade. Keller tasks Cross and Green with activating this set of prototype equipment, a displacement beacon, which through the satellite may be able to seal the dimensional rift. However, after activating the beacon, both characters are caught up in a "harmonic reflux", a distortion caused by the rift. Despite this, Cross and Green are able to return safely and Keller congratulates them on their success.
Bonus Chapter:
The unlockable vortigaunt mission provides background information explaining how the orange crystals used by the rift-sealing machine in Half Life: Decay are acquired and used by the Nihilanth during the final boss battle in Half Life. The two player-controlled vortigaunts battle through Marines and Black Ops in the underground Black Mesa complex to find the orange crystals in the back of a military van. At this point the screen fades and the mission is declared a success; it is presumed that the Nihilanth warps them back to Xen and installs the crystals in his cave.