The Nihilanth was the leader of the Xen creatures that resided on Xen and had control over the Vortigaunts, Alien Grunts and Alien Controllers. He led an attack on the Black Mesa Research Facility after a failed test opened up a portal to the alien borderworld. Nihlanth was killed by Gordon Freeman in order to seal the portal that the Nihlanth kept open, although this led to portal storms appearing across earth and the eventful arrival of the Universal Union.
In an altered timeline, Viktor Rascalov used a time machine to go back just prior to the Black Mesa Incident and make a deal with Nihlanth to send his Xen forces to present day (around a decade into the future) and spare him from perishing. Nihlanth agreed, although he still launched his attack on the facility. Viktor returned from his present time to the Black Meas Incident in order to link up the portal to the modern day earth, although found himself being chased down by Nathan Johnson and Alyx Vance (as Viktor had kidnapped Nathan's daughter Samantha. Viktor set up a portal in the Nihlanth's chamber. Nihlanth betrayed and killed Rascalov and was about to teleport himself and his Xenian forces into the future, but was stopped and killed by the combined efforts of Nathan and Freeman.
Despite being blown up, particles and DNA relating to the Nihlanth were found by a survey team exploring Xen and they began to work on reviving the Nihlanth's species. They were interested in his telepathy and immense power and wanted to utilize it. Fifteen years later a successful fetus of the Nihlanth race was created and kept contained in a jar, with the plan to mature it and use its knowledge. However the research scientist working on the project was killed by The G-Man, who then took the fetus to use it for his own agenda.