Unfortunately, though Black Mesa has been obliterated, Earth has yet to feel the brunt of this disaster. "Portal Storms", a seeming side-effect from the resonance cascade, form a dimensional rift between Xen and Earth. These Portal Storms spread outside the confines of what is left of Black Mesa and throughout all of Earth, providing temporary, chaotic, and destructive links between Xen and Earth. Aliens (from Xen) of all types are teleported into suburbs. Headcrabs crawl along the aisles of grocery stores while others teleport into swimming pools and homes. Utter chaos erupts on Earth. The freed Vortigaunts use these storms as a ticket out of Xen and onto Earth, fleeing from the Combine.
A huge population shift occurs as people move into the cities, protected by soldiers and barbed wire fences, to escape the monsters. A feeling of safety comes over the people of Earth, as they can once again live normal lives within the confines of the cities, as the alien species continue to infest the outside world. Vast networks of ant-lion nests are formed throughout the Earth's crust, housing millions of new species.
The Combine, who have been keeping an eye on Earth since the resonance cascade, finally decide to take action. They plan on taking the Portal Storms to their advantage and use them as a method to mount an invasion on Earth. Now that Nihilanth's race have fled from the border-world to Earth, the Combine can forget about Xen and enslave both Mankind and Nihilanth's race in one fell swoop, on Earth.
Forcing space-time and the portal storms wider open, The Combine launches a multi-pronged, all-out assault on the entire Earth. They teleport troops as well as drop-ships, gun-ships, and striders from Combine off-world outposts through the Portal Storms, and onto Earth. Once there, the Combine uses the same technique that they used on Xen on the humans, building a super-army out of the combination of the DNA of the most dominant species on Earth (the humans) and Combine technology.
The primary Citadel is established in City 17. This enormous structure is home to the Earth based Combine control center. Combine armies are produced here as well as vehicles and armaments. Combine presences are established in other cities around the world. (It is hinted that there may be other secondary Citadels around the world, linked by a network.)
While fighting each other, the humans and Combine also have the threat of Nihilianth's race. The freed Vortigaunts ally with the rebel forces, wanting revenge against the Combine. The headcrabs, being headcrabs, just attack anyone they can find. Other monsters find their place assaulting both Man and Combine.
The next stage of the Combine's plan takes root. Wallace Breen, "made" optimistic about the Combine takeover, is appointed the Administrator of Earth, acting as a puppet for the Combine. How he is selected for this role is unknown at this time. Breen's first act is to surrender Earth to the Combine, explaining that the Combine have arrived for good, to immortalize humanity, convinced by the Combine that the loss of life is inevitable in this transition period as Earth joins the Universal Union. Breen formally "surrenders" Earth after 7 hours of combat between Mankind and the Combine. Breen being a human helps the Combine, too. He is a species-specific leader - this helps propagate the lie that the enslavement of humans is a positive step forward, and humans, seeing a human in power, can be more readily coerced into their new lives.
Most of the major population centers of Earth are destroyed. Those still alive move into the country, spreading out to avoid Combine capture. Small pockets of rebel fighters surface, but have to establish bases in un-safe areas in the country, where the Xenians have manifested themselves, finding niches in Earth's ecosystem. Still under the spell of the Combine, and ignoring the massive genocide, Breen views the building rebel force as a group of short-sighted troublemakers.
The remaining populated areas are named City 1, City 2... City 17, City 27, etc and are placed under control of the Combine, who are establishing a huge presence on Earth. The United Nations in New York City is taken over and destroyed.
Wallace Breen takes residence in the top floor of the City 17 Citadel, under the close counsel of the Combine, attempting to quell the rebels. Breen attempts to console humanity by permanently making a connection between himself and it. He does by controlling the media. Huge television screens are erected in city centers. Newspapers, television, and other forms of communication are censored and their content is controlled.
Breen's message is simple: That humanity should not attempt in any way to cause friction in the transition period as mankind integrates itself with the Combine. He believes in order to join this Universal Union, Man will have to sacrifice a lot, but he still believes that the ends justify the means. He truly believes that joining the Combine will be positive to humanity, and tries to convert the rest of it to his point of view. After The Portal Storms, mankind are in such disorder that they can and will believe something like this.
Ruling by fear, the Overwatch assure to continue to protect human city centers from the outside aliens, and thus fearful humans continue to live in the cities out of fear for their families and themselves. The Overwatch's brutal reign begins.
The Combine's purpose with Breen is also simple. His purpose now is to prepare Earth for an eventual total Combine migration. His job is to eliminate any resistance to the Combine. Using controlled raids and a "civil-protection" force, Breen captures and converts any resistance to stalkers [for definition, see Expanded Info section], human slaves. Additionally, the Overwatch attempt to re-enslave the Vortigaunts, with some success. The Combine's ultimate purpose is to convert all of humanity into stalkers, and all of the vortigaunts into the slaves they were before Gordon freed them.More important minds are taken to Nova Prospekt, where they are stored in containment and experimented on - the Combine want to get as much knowledge out of humanity as they can before they destroy it. All of these things are leading to a drastic change in the purpose of humanity - it is about to become a slave race.
The Combine Overlord orders some transitional tasks, above and beyond Breen's power. First of all, the Overwatch enact a Suppression Field to prevent humans from procreating. (In particular, protein chains important to the development of an embryo were specifically blocked.) They do this so no new humans can be born, and that the humans left on Earth will be the final generation of them. They also put a biochemical in the water supply to make people gradually forget the past, and so they can more easily comply with Breen and the Combine - to forget why they hate them. Finally, the Combine begin to drain Earth's oceans. These tasks show that the Combine are preparing Earth for new residents.