Following the death of the Nihilanth, the Vortigaunts have chosen to ally themselves with the human-led Resistance in its bid to overthrow the Combine rule of Earth.
GMod: Synth invasion on Xen (The Hunter VS Vortigaunt)
Long before the Black Mesa Incident, the Vortigaunts' homeworld was invaded by the Combine, forcing the survivors of the invasion to flee to Xen. When the Black Mesa Incident occurred, their master, a being known as the Nihilanth, viewed the rift that opened as a chance to escape, and directed the Vortigaunts to invade Earth.
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