Combine occupation of Earth
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The Combine Occupation of Earth began in the aftermath of the Seven Hour War, some time after the Black Mesa Incident. Former Black Mesa administrator Wallace Breen managed Earth's surrender, thus allowing the Combine to seize power. He was then declared Interim Administrator of Earth, a largely symbolic position.
During the Combine's rule, the remnants of the human race were spread all around the world, in Combine cities, built from the remnants of Earth's devastated cities. The extent of the Combine's brutality during the occupation is not yet known, but it is believed that the Combine perpetrated genocide against mankind, installed a worldwide sub-imperial military and police force known as the Overwatch, drained Earth of its natural resources, and put an end to all human reproduction through a planet-wide suppression field.
Around 20 years after the Black Mesa Incident, the occupation was compromised, when, following the destruction of Nova Prospekt, a massive uprising was born in City 17. This uprising was spearheaded by organized Resistance forces, led by former Black Mesa scientists, such as Eli Vance and Gordon Freeman.
The events surrounding Gordon Freeman's arrival in City 17 until the Resistance's successful defense of the White Forest rocket base transpired over the course of one and a half weeks, in an area of several dozen square miles, from City 17 to Nova Prospekt on the coast. It is understood that this uprising was the first of its kind in 20 years, and that news of it reached far and wide by the time the Resistance launched its rocket into orbit and shut down the Combine's infant superportal. This act, for the first time since the Combine's invasion, stranded the entire Combine presence remaining on Earth from its home world. No further communication was possible between the Combine Overworld and Earth. News of this was certain to become global among the human inhabitants of Earth, and similar uprisings in cities around the world could be expected.
The Black Mesa Incident caused Portal Storms to erupt all across Earth, attracting the attention of the Combine Empire. The Combine's motive for invading Earth is unknown; it is surmised that the Combine simply wished to take control of Earth's resources and enslave its population, as it had done many times before to other universes. The Combine invaded Earth, quickly defeating the planet's armed forces in the Seven Hour War. Dr. Wallace Breen negotiated a surrender on behalf of the surviving human population; he was instated as ruler of Earth, and aided the Combine in rounding up the civilian populace into large, tightly controlled cities. Breen chose City 17 as his de facto capital, and the Citadel was embedded there to house the apparatus of the new government. It is likely that what was left of Earth's armies were assimilated into the Combine's occupational force.
The new rulers of Earth governed with an oppressiveness bordering on the genocidal; indeed, such was the calculated brutality of Combine rule that it seems likely that the alien rulers did intend to run Earth and the human race into the ground, despite Breen's assurances otherwise. Dissenters were turned into Stalkers or simply killed, and a reproductive suppression field was installed to prevent humans from breeding. This was coupled with a gradual leeching of the planet's natural resources, notably in the drastic drainage of the Earth's oceans. At the time of Gordon Freeman's entry into City 17, the Combine's army on Earth consisted entirely of processed humans, post-humans and military Synths.
In response to the Combine take-over, a number of the subjected formed the Resistance, a loose band of guerrillas, outlaws and spies dedicated to overthrowing the Combine. Unable to take on the Combine directly, the Resistance instead worked at undermining it by infiltrating the ranks of Civil Protection, smuggling weaponry, setting up a sophisticated 'underground railroad' with bases at Ravenholm, Black Mesa East, White Forest, and the Coast, and by helping civilians escape the Combine controlled cities. The Combine suppressed the Resistance at every available opportunity, most notably in the case of Ravenholm, which was subjected to a massive Headcrab bombardment with only one known survivor. Although the Resistance had some successes, according to Judith Mossman the Combine was largely aware of the Resistance's activities, and only allowed its continued existence because it didn't consider the rebels an appreciable threat.
Five years prior to the return of Gordon Freeman and during construction of the Citadel, the Combine managed to locate The G-Man in an apartment complex located in the City 17 Quarantine Zone. The Combine haphazardly imprisoned him in a Vault hovering over the QZ, powered by energy harvested from captured Vortigaunts. The Combine made plans to relocate the G-Man but encounter delays. After discovering the Vault and mistakenly believing the individual held inside might be Gordon Freeman, Eli and Alyx Vance set out to release him. Despite the Combine's efforts to stop her, Alyx manages bring down and infiltrate the Vault and open the cell, unknowingly releasing the G-Man. There, the G-Man shows Alyx a vision of the future when her father Eli is killed by a Combine Advisor at White Forest. The G-Man lets Alyx intervene, killing the Advisor and saving Eli, changing fate and the ending of Episode 2. He then tells Alyx that she has proven herself valuable and would be a good replacement for another who has failed or refused to do G-Man's bidding, showing her a glimpse of Gordon. He then leaves her in stasis to "await assignment."
Return of the Freeman
Gordon Freeman arrived in City 17 - approximately 20 years after the Black Mesa Incident - at the City 17 Trainstation. He was fortunately intercepted and rescued by Barney Calhoun in his Metrocop disguise when he was about to board a train to Nova Prospekt. Calhoun immediately sent Freeman to Dr. Kleiner's lab, where they planned to send him and Alyx Vance through the teleport to Black Mesa East. An unfortunate malfunction made Dr. Breen and the Combine aware of Dr. Freeman's return. Due to his almost single-handed defeat of the Xen armies in Black Mesa and then his sudden disappearance, he had become a figure of legend amongst the Resistance forces and the civilian populace. His sudden reappearance caused a mass celebration amongst the civilians, and a fit of hysteria amongst the Combine. During a panicked attempt to locate Freeman, the Combine deployed thousands of Scanners, Gunships, hunter-choppers and Civil Protection units. The CPs began to systematically destroy all known resistance bases, effectively silencing them, but failing to stop Freeman. Freeman, on the advice of Calhoun, made his escape through the canal and sewer system, home of the Underground Railroad. At this time, the Combine attacked several railroad stations, effectively ending the railroad, with only a few fortunate survivors. Freeman himself managed to escape City 17 by use of an Airboat, arriving later at the Resistance base Black Mesa East and meeting up with Eli Vance.
Dr. Breen was determined to capture Freeman and launched a raid on Black Mesa East, capturing Eli Vance and several core Resistance members, acting on intelligence provided by double-agent Judith Mossman. However, Breen was unable to capture Freeman - who escaped to Ravenholm - and was reprimanded, but he was able to convince the Combine that Dr. Vance's capture showed the effectiveness of Overwatch troops. Breen then pressed the Overwatch troops to increase their efforts to capture Freeman, taunting them and threatening to send them off-world. The Combine then turned its attention to the Resistance bases along the coast, launching failed attacks on Shorepoint and New Little Odessa but capturing some abandoned posts as well as Lighthouse Point. At this time, Freeman followed the coastline in the Scout Car to meet Alyx Vance (en route by train) at Nova Prospekt to rescue Eli Vance.
Attack on Nova Prospekt
After crossing the Antlion-infested coast to the Vortigaunt Camp, Freeman acquired the Bugbait with the help of a Vortigaunt ally. Freeman used this new tool to call an army of Antlions to follow him. Freeman and the Antlions breached Nova Prospekt's coastal defenses and then infiltrated the prison. The Antlions laid waste to the forces in the prison, while Freeman was able to meet Alyx at the train depot. Together, they located Vance and Mossman, but learned the terrible truth that Mossman was a double-agent. Using Mossman to activate the Entanglement teleport, they were betrayed once again as Mossman teleported herself along with Eli Vance to the Citadel. Freeman and Alyx Vance quickly reactivated the teleport as Overwatch troops broke into the chamber, their attacks damaging the teleport. As the two teleported away, the teleport itself exploded, destroying the prison in the process. The damage was felt, possibly both metaphorically and literally, by citizens in the nearby City 17.
Battle of City 17
Up to this point, the uprising consisted of Combine raids and attacks on Resistance-held bases along the coast and around the perimeter of the city. The destruction of the Nova Prospekt research labs and the Combine's only teleport prompted the Resistance to launch an attack on the Combine forces and the Citadel itself. Freeman and Vance's destruction of Nova Prospekt demonstrated to the civilians throughout City 17 that open aggression against the Combine would not necessarily result in the Resistance's annihilation, and that a full-scale uprising against the Combine could conceivably defeat it and wrest Earth from its control. Nova Prospekt was one of the Combine's most heavily guarded and impregnable strongholds, and Gordon Freeman and Alyx Vance, just two members of the resistance, assaulted and defeated the Combine on its own ground. While most Resistance troops attempted to liberate the city, Barney Calhoun led a mission to rescue Eli Vance, whom they learned from the Vortigaunts, was held captive in the Citadel. For over a week the increasingly large and determined resistance army was locked in bitter urban combat with the Combine forces, engaging in bloody street-fighting. Civil Protection found themselves hard pressed and unable to control the uprising, and Overwatch reinforcements were sent in. At the time of Freeman and Alyx's return, the Resistance was in control of suburban areas, while the Combine controlled the city center and other pivotal buildings. The city itself was heavily damaged from the toll of the battle. Despite the Combine's obvious technological superiority, it could not gain the upper hand over the Resistance cells.
Freeman and Alyx were lost in a teleportation loop for over one week, and all but presumed dead in the destruction of Nova Prospekt, but the civilian population of the City joined the Resistance en masse and began the uprising in their absence regardless. When Freeman and Alyx returned to the city, Freeman and Calhoun combined their leadership skills and began to turn the tide against the Combine. Freeman led the attack on some of the final Civil Protection barricades and CP-controlled buildings before using the city's tunnels to travel quickly to the city center. At this point, the Resistance were caught in an intense Overwatch counterattack. Resistance positions were bombarded by Headcrab Shells, destroyed by Striders, and tougher troops. The assaults towards the center of the city caused intense damage to the buildings, due to the Combine's usage of pulse artillery. Thanks to Freeman, the Resistance was able to overcome the attacks and press on to the city center after breaking through a generator-powered barricade. Unfortunately, Alyx Vance was captured by the Combine whilst scouting for a route on a rooftop.
Now in the city center, the Resistance launched an attack against the Overwatch Nexus, the center of Overwatch activities. Its capture was intended to impair Overwatch's movement and coordination, and open several gates for the resistance, as well as eliminate a powerful Combine Suppression Device on the roof. Freeman and Calhoun destroyed the power-generators and opened the building for Resistance reinforcements. The Combine attempted to recapture it with Striders, but following an intense battle, the Resistance, led by Freeman, defeated the Striders and secured the Overwatch Nexus. This allowed the Resistance to attack the base of the Citadel, where the Combine infantry was pulled back, and defense was turned over to the Striders and Gunships. The Synths inflicted heavy casualties on the resistance, but even they could not keep the rebels at bay; Freeman led the final charge toward a prominent horse statue, destroying two Striders in the process, and then penetrated the Citadel.
Once inside, Freeman allowed himself to be captured, arriving at Wallace Breen's office after having been stripped of his weapons. Mossman, feeling guilt at allowing Eli Vance to be captured, rebelled against Breen, apparently having only feigned her allegiance to him. She freed the captured freedom fighters, forcing Breen to attempt to use the Citadel's reactor to teleport to the Combine Overworld. Freeman overloaded the reactor, causing it to explode, killing Breen and tearing the entire top section of the Citadel away. Vortigaunts rescued Alyx and Freeman just in time, burying them in the rubble at the base of the tower. The damage inflicted on the reactor had caused most Combine technology in the city to come open to cybernetic attack, and the forcefields around the city dropped, allowing thousands of creatures to swarm in, mainly Antlions. A more widespread implication of the Citadel's destruction was a dampening of trans-dimensional Combine communication technology worldwide, isolating Combine forces on Earth.
The Combine began to withdraw their forces from City 17, leaving behind some infantry units and their reserves of Civil Protection forces to stall the Resistance's escape. Alyx and Freeman managed to partially stabilize the Citadel reactor, giving more time for the remaining Resistance forces led by Calhoun to evacuate. However, the Combine and the increasing swarms of Antlions were not making evacuation easy. The Combine reserves in the city were defeated in open battle by the Resistance or led away by Alyx and Freeman. They and Calhoun escorted the last of the citizens to the final trains of refugees evacuating the city. The Combine advisors were evacuated in escape pods just as the Citadel exploded, virtually annihilating the remains of the City and all those left within.
Battle of White Forest
The destruction of the Citadel had caused an infant Superportal to begin forming, which, once mature, would allow massive reinforcements from the Combine Overworld to pour through, alluded to by Eli Vance when he said, "It'll be the Seven Hour War all over again, except this time we won't last seven minutes!" referring to the fact that if these reinforcements made it through, they would easily crush the remaining Resistance forces, whom the Combine were now struggling to overcome. It was later revealed that this had been the Combine's plan since the detonation of the Dark Fusion reactor. However, Alyx and Freeman managed to obtain the data planned to be sent to the Combine Overworld, which the Resistance could use to close the portal. The Resistance forces evacuated their refugees and troops to the Resistance base of White Forest, where they were planning to use the Xen Relay Network to close the Superportal. Alyx and Freeman were forced to fight their way through the hordes of Antlions that had colonized the vast mines near White Forest. During their journey, they found they were advancing to White Forest in tandem with a large Combine force on its way to attack the base. Alyx was mortally wounded near a mine by a Hunter, but fortunately revived with the help of several Vortigaunts.
In order to beat the Combine to White Forest, Alyx and Freeman obtained a car to race there. At one point, they discovered an Advisor, but were unable to kill it before it escaped. Upon reaching the White Forest Inn, Combine soldiers supported by Hunters ambushed and attacked them but were fought off, taking heavy casualties. The two then reached White Forest, where they found a crashed Combine dropship carrying a single Strider, which was defeated by Dog. Alyx and Freeman turned over the data packet so Magnusson and Kleiner could make the final adjustments to their rocket. Soon after, Combine soldiers directed by an Advisor raided White Forest through the secondary silo, but again were repelled by Freeman and the silo was closed just in time. Soon after the raid, Magnusson realized that they could not finish their rocket before the Combine attacked. In retaliation to this adversity, the able-bodied Resistance members prepared for defense and Magnusson directed Freeman in the use of the Magnusson Device. This made real resistance against the Striders possible, since without the Devices the Resistance would have been forced to use woefully inefficient RPGs. The main body of the Combine attack, consisting of a company of Striders supported by packs of Hunters, launched their attack on the base. Making use of the Magnusson Devices, Freeman eliminated all the Striders, allowing the launch to go ahead safely. The rocket was launched and successfully used to seal the Superportal, stranding the remaining Combine forces on Earth.
Following this victory, Alyx and Freeman immediately prepared to leave White Forest to pursue Dr. Judith Mossman. The Resistance leaders discovered from the data packet retrieved by Alyx that Mossman had located the legendary research vessel Borealis. Mossman was in trouble and the two were determined to beat the Combine to the Borealis. Unfortunately, before departure, the White Forest Hangar was attacked by two Advisors, one of which killed Eli Vance before being driven off by Dog.
Due to Alyx's actions in opening the Vault and freeing the G-Man 5 years earlier, Eli's death in Episode Two is prevented. Consequently, at the time of his original death, Alyx is taken by the G-Man at this same moment and put into stasis to "await assignment". Eli and Gordon are left in the White Forest hangar, with the Advisor dead and Alyx missing. Eli expresses his frustration, vowing to kill the G Man for this. He hands Gordon his crowbar, telling him "We have work to do".