The Combine Empire invades and takes control of the Vortigaunts' homeworld (which we have never seen), and attempt to enslave them, including their leader, Nihilianth (who is not necessarily a Vortigaunt). A long and bitter struggle ensues, as the Vortigaunts flee from planet to planet, battling and evading the Combine forces. With their backs against the wall, they flee to the border world Xen, where they wait their demise. Xen is sort of like a "subway station" of the universe in that it can be used to cross dimensions. Marc Laidlaw calls it "a dimensional transit bottleneck--an area of continual contention."

(A quick note about Xen: Marc Laidlaw has stated that "nothing is native to Xen" which implies that life Xen is a mish-mash of beings from all over the universe, being willingly or unwillingly transported there. I will refer to the beings from Xen as the "Xenians", which include the headcrabs, ant-lions, vortigaunts, the race that Nihilianth commands, and so on.)

The Combine attempt to hybridize the dominant species of the planet (In Xen's case, the Vortigaunts) with their own technology to create a "Super soldier" that is adapted to Xen's environment and uses powerful Combine technology. (This is what they attempt to do on Earth, as well). Nihilanth and his people fight bitterly against the Combine.

Back on Earth, Gordon is studying for his doctorate at MIT. At Black Mesa in New Mexico, teleportation experiments are taking place. Under the supervision of researchers Eli Vance, Arne Magnusson and Issac Kleiner, crystals are retrieved from Xen, and organisms are analyzed. Research is developing.

Black Mesa's chief competitor for government funding, Aperture Science, also develops its own Portal technology parallel to Black Mesa onboard its many research facilities and enrichment centers, including the Borealis, a research vessel. One day, after what seems to be a severe mishap, the Borealis disappears completely off the face of the Earth, taking all passengers and crew with it. GLaDOS, an artificial intelligence program at Aperture Science, is made operational for the first time at one of Aperture's enrichment centers.

They're waiting for you Gordon, in the test chamber.

(i) GMan Orchestrates The Resonance Cascade, "GMan", a very mysterious figure at Black Mesa, whose motives seem to be independent of both humankind and of the Combine, triggers a resonance cascade within the Anomalous Materials sector of the Black Mesa complex, by bringing in a specific test sample to be used. His selection of this hazardous material is masked by a system crash, to cut out formal communication between scientists. The resonance cascade rips open space-time and forms a portal between Earth and Xen. Nihilanth's race sees the dimensional fissure as an escape route. Of course headcrabs and other life trapped on Xen decide to hitch a ride to Earth, for the fun of it. Black Mesa becomes chaos, as the Hazardous Environment Combat Unit, a United States Marine Corps Special Forces division, is brought in to quell the results of the Resonance Cascade, including the elimination of all humans caught in the cross-fire.

This resonance cascade is so immense in nature, that the Combine Empire notices it, turning their interest to what is happening on Earth.

One man in a HEV suit becomes of great interest to G-Man during the incident. Gordon Freeman, a newly assigned scientist in the Anomalous materials lab, shows exceptional skill in dealing with Xen beings and U.S. troops. G-Man's interest peaks as Freeman navigates through Xen (the Xenians believe that Gordon is just as much of an enemy as the Combine) and defeats the Nihilanth. G-Man is impressed.

Eventually Black Mesa is destroyed by nuclear detonation (noted in Half Life: Opposing Force). Several survivors exist, including Wallace Breen, Black Mesa's former administrator; Barney Calhoun, a security guard; Dr Issac Kleiner, a prominent scientist at Black Mesa; Dr. Arne Magnusson; Dr. Eli Vance; and of course, Alyx Vance, Eli's daughter. Alyx is of particular interest to GMan

(ii) Gordon is Hired - At the end of Half-Life G-Man, impressed by your work, gives Gordon a choice between his death or working for the G-Man. Half-Life 2 assumes he chose life over death. After you choose to work for him G-Man puts you in a slow-time-warp (i.e., you are put into stasis) to call upon you when needed.

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. [ screenshot, from Eli's lab ]

Meanwhile, all scientists have evacuated their facilities at Aperture Science, including their main enrichment center. The events of Portal take place. ¹ The 'Aperture Science Hand-Held Portal Device' is inadvertently released into the wild, however, it is not known what becomes of it.

At the end of HL2 you complete your assignment, by destabilizing the Citadel in City 17, the Combine throne on Earth. As a result, the Combine's communication network has been taken down, and the Combine forces are fractured and leaderless.

GMan tosses his pawn back into stasis. Gordon is now in hypersleep, as he has completed his job, and he is no longer needed. GMan is about to warp in and transport Alyx when he is intercepted by a group of Vortigaunts. They warp in, rescue Alyx, and transport her outside in front of the Citadel. They pull Gordon out of stasis, and transport him to a location near Alyx. Both of these things happen against GMan's wishes. The Vortigaunts have in effect taken control of Gordon, blocking GMan from intervening in Gordon's adventures. GMan has to resort to kindly asking Gordon to protect Alyx when the Vortigaunts let their guard down to save her life in Episode 2.

The Combine on Earth have lost their primary method of communication with their Combine leaders. In a last-ditch effort, they decide to destroy the Citadel in the creation of a high-energy "super-portal". In conjunction with the creation of this super-portal, the Combine need to send a transmission packet back to their homeworld detailing to their forces how to access it - what amounts essentially to a high level reinforcements request. This process will lead to the deaths of all of the rebel forces and evacuees of the city. The Combine also prepare the remaining Combine for escape via escape pods during the meltdown.

Why do the Vortigaunts pull Gordon out of stasis and place him just outside the Citadel? I believe they want Gordon to stop or at least delay the destruction of the Citadel. They want Gordon to stabilize the core reactor of the Citadel so that the rebel forces and the rest of the Vortigaunts can safely evacuate the city before it is destroyed.

Why doesn't GMan like them doing this? The way I see it, GMan wants that reactor to be destroyed as soon as possible and that transmission packet to be sent, at any cost. Why? Because it seems GMan is trying his hardest to lure the rest of the Combine forces over to Earth. This seems like GMan's plan from the beginning, the reason why he got Gordon to destroy the Citadel. This reason is to bait the rest of the Combine over to Earth so they can be fought on Earth, or so that GMan could distract the Combine while he mounts an attack on the Combine's homeworld. The way GMan sees it, hundreds of thousands of human and Vortigaunt lives will be lost in the destruction of City 17, but if that message is sent, GMan could win an interstellar war. On the other hand, the purple Vortigaunts care more about the lives of the members of the Resistance and the citizens of City 17 on Earth than winning the war.

Unfortunately for GMan, Gordon and Alyx do stabilize the core (or at least, for a few hours) to allow the Resistance to evacuate. Though, in the end, this allows the Combine enough time to send their message, as well as successfully evacuate the Combine escape pods from the Citadel, in a stunning discharge of raw portal energy, leveling City 17. These escape pods are dispersed all over the countryside surrounding the remains of City 17. As a result, the immense super-portal is now operational and is awaiting the opening of another dimensional gateway from the Combine side.

Alyx and Gordon manage to secure two transmission packets from the Citadel. On the first packet are contained the exact coordinates and instructions for the operation of setting the super-portal as a gateway to send troops. The second packet is more intriguing- exact coordinates and blueprints depiciting the location of the missing Borealis freighter. On board is believed to contain a portal technology much more advanced than Black Mesa's.

Despite sustaining a massive attack, aided by a code from the transmission packet, the rebel forces manage to launch a rocket, which in concert with the satellites launched over 20 years earlier during the resonance cascade, is able to shut down the super-portal. The Combine is held at bay, for the time being. However, as Gordon, Alyx, and Eli (unfortunately) learn, the hatched Combine Advisors are still roaming the countryside, feeding on the very rebels that are trying to take them down.

What happened next, would have been shown in Episode 3.



UPDATE September 2017: As we all know, Episode 3 never came out. And Marc Laidlaw, writer of the Half Life saga, departed Valve in 2016. A year later, he wrote a coded letter describing a sketch of some of the events that might have happened in Episode 3. Here is a version decoded with the names de-scrambled. It's definitely worth a read, and gives us a peek at what might have happened in Episode 3.

Now that Valve is finally revisiting the Half-Life universe with Half Life: Alyx, it's not clear how much of this will be canon. I guess we'll find out!