NEXUS refers interchangeably to both the faction and the NEXUS Intruder Program, a highly sophisticated computer parasite that gradually takes control of other computer systems, such as those of the New Paradigm and the Collective. It serves as the main antagonist throughout Warzone 2100, with the Project fighting against it directly in Campaign 3.
During the campaign, it is discovered that the NEXUS Intruder Program was created by Dr. Alan Reed, the CEO of the Reed Corporation, initially as a means to upload one's consciousness into cyberspace, starting in 2080, when the Synaptic Link technology was patented. However, after 3 years with little progress, the United States military, which provided funding for the Synaptic Link technology, withdrew its financial support for the NEXUS Intruder Program. This infuriated Dr. Reed, who swore to have his revenge on anyone that stood in his way.
According to NEXUS, it was responsible for initiating the Collapse. It is presumed that Dr. Reed was ultimately responsible for the Collapse.
Eventually, the Project successfully destroyed the Laser Satellites and the nuclear missile silos that NEXUS commandeered in his efforts to destroy the Project, and destroyed his main base of operations. However, despite this, NEXUS may not have been truly defeated...