2000- The Combine invades and takes control of the Vortigaunts' homeworld in an attempt to enslave them. The Vortigaunts fight back though, but eventually flee and planet hop their way across the galaxy while fighting the Combine. When it is apparent that they have little to no options, they flee to Xen. Xen is the melting pot of the galaxy and apparently has some sort spacial significance to portals all over the galaxy. It is suggested that this is a sort of spacial flux where portals are drawn. This is were the majority of your enemies come from in HL1, such as the headcrabs and ant-lions.
The Combine attempt to incorporate the highest life form of Xen (the Vortigaunts) into their "Universal Union" by implanting them with Combine tech to make a super soldier. The reasons for this are abundant such as the fact that native species will be able to tolerate the atmosphere, navigate the cities, etc... Nihilanth, the Vortigaunt leader, fights back against the Combine. Over time the Vortigaunt start to loose and start looking for one final escape route to try and bide their time. Fortunately, they will get one soon.
Meanwhile on our lovely little planet, Gordon Freeman is studying for a doctorate degree at MIT. Meanwhile, at Black Mesa in New Mexico (a decommissioned missile base), teleportation experiments are taking place. A portal is successfully opened to Xen under the supervision of researchers Dr.Kleiner and Eli Vance. They take the opportunity to retrieve crystals and life forms from Xen for study.
Back on Xen, the Vortigaunts (and Combine) discover Black Mesa's portal from Earth. The Vortigaunts finally have their escape route, but the Combine see it as another opportunity for invasion. Through the portal they contact Wallace Breen, the Administrator of Black Mesa. The Combine convinces Breen (through bribery) to allow them to bring Earth into their "Universal Union", stating that it is mans right and destiny to be able to advance into the stars. Breen falls head over heals for their propaganda, truly thinking this is the best way to better humanity. Meanwhile, the Combine ready for an assault on Earth.
2005- Wallace Breen, under supervision by the Combine Overlords, triggers a Resonance Cascade within the Black Mesa complex, by selecting a certain test sample to be used. Also, the anti-mass spectrometers used during the test had a capacity of 80%, and they were pushed to 105% for this sample. (That was another large part of the problem, not just the specimen used.)
Breen's selection of this material is covered by a system crash, which Breen triggers to stop communication between scientists. The G-Man is aware of Breen's plan and tries to prevent the Resonance Cascade, but fails. This "volatile portal" allows the Combine to send their initial forces to take over Black Mesa and prepare for the main invasion. The Vortigaunt use the portal for their escape to Earth. Headcrabs and other life on Xen decide to come along for the a ride as well. The G-Man prepares a task force to close the main portal and rallies up US soldiers to fight the aliens.
Gordon Freeman, a newly assigned scientist in the Anomalous materials lab, is the one that activates the substance which triggers the Cascade. He soon becomes of great interest to G-man as he fights his way through the Black Mesa Facility. (The Anomalous Materials Lab is were testing and research went on with specimens brought back through the portal.)
Gordon has no idea what is going on and launches a Lambda Satellite into space prior to the Cascade under orders from Breen.Unfortunately, this is what the Combine need to start the Portal storms by opening up portals all over the Earth.
Black Mesa is then destroyed by a nuclear blast, but the Combine have what they need- a portal to Earth and a satellite to conduct a portal storm with.
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 stasis to call you when needed.
Okay, now I'm going to break these posts up. The following post describes what happens when the Combine start to gain control of the population, what their plans are, and how they deal with uprisings and rebellion.
2007- Black Mesa has a huge ripple effect on the rest of the world after the events of Half-Life 1, as the Combine gradually open up portals world-wide, via its portal-network satellite. Aliens from Xen are teleported onto the Earth and chaos erupts. The freed Vortigaunts flee to Earth to escape the Combine, which are struggling to regain control of them.
A huge population shift occurs as people move into the cities, protected by soldiers and barbed wire fences, to escape the monsters.
Meanwhile, the Combine prepare for an assault on Earth, knowing that the required portals are ready. Now that the Vortigaunts have fled from to Earth, the Combine can forget about Xen and enslave both Humanity and Nihilanth's race in one fell swoop- on Earth.
2009- Using the portal network as transport gateways, the Combine launch an all-out assault on the entire Earth, teleporting troops as well as drop-ships, gun-ships, and striders from Combine off-world outposts. 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 (humans) and Combine technology.
The Combine control center on Earth, the Citadel, is established in City 17. Combine armies, vehicles, and weapons are produced here. The Combine take hold of other major cities around the world and it is hinted that there may be other secondary Citadels around the world, linked some sort of network.
The freed Vortigaunts ally with the rebel forces, wanting revenge against the Combine. The other monsters let through the portals find their nich in the ecosystem and attack both sides without preference.
Now the next stage of the Combine's plan can begin. Wallace Breen, still optimistic about the Combine takeover, is made the Administrator of Earth (which was promised back in Black Mesa by the Combine). Breen surrenders Earth to the Combine, saying that the Combine are here for good, to immortalize humanity and lead them toward their destiny. Even though he sees the death and abuse of humans, he believes that the loss of life is inevitable during the time the Combine are taking charge and Earth is integrated into the Universal Union. Breen "surrenders" Earth after 7 hours of fighting the Combine. Breen being a human helps the Combine as well. It is more easy for humans to accept him and it makes the population more easy to be fed things that are not in their interest.
Most of the largely populated areas of Earth are destroyed. People start moving into the country to avoid Combine capture. Rebel fighters start to emerge and fight back. Still under the influence of the Combine, and ignoring the genocide, Breen sees the rebels as short-sighted troublemakers.
The Combine now start renaming their captured cities- City 1, City 2... City 17, City 27, etc... The United Nations in New York City is destroyed as well.
2009- Breen moves to the top floor of the Citadel, attempting to calm the rebel and stop the attacks. He does this by taking control of the media. Huge television screens are built and put up in the largely traveled areas of the city. Newspapers, television, phones, and other communication methods are controlled.
Breen's message is simple: Humanity shouldn't attempt try to prevent, in any way, Earths combination with the Combine. He thinks that to join the Universal Union, everyone will have to sacrifice a lot, but he still is convinced that it will all turn out for the common good. After the Portal Storms, everyone is in so much disorder that they ae ready to accept anything that offers even the smallest promise of help.
Ruling by fear, the Combine Overwatch assures that they will keep protecting the humans and that it is unsafe to go beyond the city fence. So the fearful humans keep living in the cities out of fear for their families and themselves. The Overwatch starts their harsh ruling.
The Combine's purpose with Breen is also simple. His purpose now is to prepare Earth for the Combine and to eliminate any resistance to the them. Using controlled raids and a "civil-protection" force (much like the secret police), Breen captures and turns any resistance into stalkers- human slaves. Meanwhile, the Overwatch tries to re-enslave the Vortigaunts, with lttle success. The Combine's main goal is to convert humanity into stalkers, and all of the vortigaunts into slaves like they were before Gordon Freeman freed them. Smarter humans such as scientists and engineers 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.
The Combine Overlord orders some tasks, above Breen's power. First off, the Overwatch put up a Suppression Field to prevent humans from mating. They do this so no new humans can be born, and that the humans left on Earth will be the last. They also put a chemical in the water to make people slowly forget the past so they can more easily comply with Breen and the Combine. Finally, the Combine start draining Earth's oceans to prepare Earth for new residents.