Let me explain some of the finer details of the second theory which I subscribe to. The Nihilanth is sort of a queen of the Vortigaunts, who is able to control them telepathically. The Vorts are hive minded (I refer to the official game guide), and they are coterminous, meaning they have a shared mind. The Nihilanth has more influence in this shared mind, and is thus able to control or guide the entire Vortigaunt race. The Combine captured the Nihilanth at one time in the past, and made some modifications to it to rear it under Combine control. The evidence of this is all over the Nihilanth's body, as there are many stitches where someone was making surgical modifications. The Nihilanth is analogous to Dr. Breen, being a puppet leader of the Vortigaunt race. The Combine uses Nihilanth to act as a medium in dealing with the Vorts, just as Breen was used as a medium for dealing with humans. Someone within the Combine made a deal with Breen sometime before the resonance cascade. What came of this was Black Mesa's acquirement of an alien crystal, that when bombarded with phaser rays, would tear a hole in the dimensional fabric, allowing the Combine to move in en masse and conquer. Breen influenced Black Mesa to perform a "test" on the crystal, as dictated by the Combine. Breen may have made contact with the Combine as a result of scientists exploring the Combine outpost on Xen, with their presence there alerting the Combine masterminds that another race ripe for conquering existed somewhere in the multiverse. To get back to the matter of the Vortigaunts, the Combine used it's influence on Nihilanth to cause the Vorts who were on Xen to invade Earth after Breen successfully orchestrated the resonance cascade. The Vortigaunts wreaked havoc on the planet, until Gordon destroyed Nihilanth at the end of HL1. The result of this victory was that the Vortigaunts became able to think for themselves, free of Nihilanth's influence. Recognizing that Gordon freed them from bondage, the Vorts came to revere him, and they also realized that they had to assist the humans, because the Combine had many other slave races other than the Vortigaunts, and they were about to send more waves of dominated aliens to continue the attack against Earth. This happened, and Earth was defeated. Ever since then, humans such as Kleiner and Eli Vance have conspired with the stranded Vortigaunts to topple the Combine. Just as extra information, there is some controversy over the Alien Controllers who were present on Xen, and appeared to be domineering over the Vortigaunts. My speculation is that being a hive-minded race, the Vortigaunts have a caste system similar to most colonial insects. The Nihilanth is a queen, the vorts are workers, the grunts are soldiers, and the controllers are drones. All four of these creatures are similar in anatomy if you look at their third protruding arm. This feature suggests the possibility that these are all different castes of the same race. The roles of these creatures as seen in HL1 reinforce this. Vorts are seen working in an alien factory on Xen, Grunts are obviously used as heavy weapons, Controllers are serving as the ruling elite, acting as taskmasters in the factories (you could say these guys are like the Combine Metrocops), and then you have the big leader, Nihilanth, directing everyone else.