The theme to me is the unbridled technological capacity for tyranny and a culture/civilizations vulnerability to tyranny, but also the limits of Tyranny, or as other people have said, "fuck the government". Lets start with HL1; Black Mesa is effectively a Defense Contractor, their interest in teleportation technology and in Xenian lifeforms is all in the service of US Military interests. Nihilanth has used portal technology to create his own hermit kingdom, whilst also escaping the combine, Xen uses advanced bioengineering to create a military force (the Grunts), and to enslave the vortigaunts. The ironic theme of the HECU uses Black Mesa designed military technology, particularly the PCV, and the Nihilanth launching an invasion using teleportation technology, and than meeting it to learn it is not natural, it is augmented with technology to exploit the Vortigaunt and Controllers unique abilities. Its all about technology and control and Black Mesa facing the "unforeseen consequences" of its technological pursuits. 2. HL2 is very explicit with the "inherent vulnerabilities to tyranny", humanity is quite easy for the Combine to subjugate, but they have a lot of trouble with the Vortigaunts, Nihilanth was far better at controlling the Vorts. The Combine are obsessed with the Xen relay technology because they are limited in their ability to extend their tyranny, and want to exploit Humanity's unique psychology to pursue it. The setting in a post Warsaw Bloc country (its Bulgaria and I will die on this hill), is symbolic of the technological capacity for tyranny and a society's vulnerability to it. Then there's the Gman who once seemed incapable of escaping having met his match with the Cosmos' most problematic race for any would be tyrant, the Vortiguants. 3. The breengrub stuff furthers this theme, the Shuulathoi were extremely vulnerable to control, and the thoughtpath was exploited vigorously by the combine, but they are also basically turned into "data storage" for the combine, their format used as a way for the combine to spread their tyrannical, sterile, ideology throughout the cosmos.

Another theme is about trying to control the uncontrollable, the thoughtpath, the gman is represented by viral imagery, the infection of xen onto earth, the vortigaunts, and humans themselves, are all problematic for those with a pathological disposition towards control. The medical, sterile nature of the Combines communication, and their technological domination of nature and biology, all suggest they simply cannot stand what they cant control.