Part of the resilience which got Dr. Isaac Kleiner through the resonance cascade and the following two decades might have to do with, depending on his age (which doesn't seem to be attested anywhere), either having been part of the German Jewish diaspora which took place in the mid- to late 1930s, or being a first-generation descendant of someone who was.
In Episode 2, the G-Man plants a suggestion in Alyx's mind while she is unconscious so she will relay the message "Prepare for unforeseen consequences." to Eli when she and Gordon reunite with him. After she does this, Eli shoos her out of the room by asking her to go make some tea so he can reveal to Gordon in private that the G-Man himself whispered that very warning into his ear right before the resonance cascade. In the original Half-Life 1, the name of chapter that begins when you wake up after triggering the resonance cascade is titled "Unforeseen Consequences".
When DOG gets all jittery after the rocket launch he's detected the incoming Advisors and is trying (unsuccessfully) to stop them.
It's easy to overlook what the take-off weight discrepancy means: Lamarr, of course. (And the Gnome, provided Gordon returns to White Forest with it.)
The plot of the game's first few chapters (Gordon shows up while Barney's on duty, preventing him from going to Nova Prospekt and being stalkered; Alyx is around to save him from a squad of Civil Protection; Kleiner's teleporter has just been completed) seems a little forced and coincidental - which it is, because the G-Man has made sure all his pawns are in order before Gordon's time comes again.
The name given to the main alien threat (the Combine/Universal Union): they Combine their technology with other species and are creating/trying to create a Universal Union by doing so! They also sweep across worlds, harvesting their resources.
The fact that just before the moment when you stop running from the Combine and start actually attacking them (the attack on Nova Prospekt is the first time Gordon pro-actively attacks the combine in the game,) you go past several bunkers reminiscent of those used by the Germans in D-Day, which was the beginning of a large scale allied offensive campaign.
Even the first words you hear in the course of the game are prophetic. "Rise and shine, Mister Freeman. Rise and shine." Given it's the G-Man who says them, it sounds like a mocking greeting to someone who's slept a while, and really, there's no reason why it couldn't be. However, considering what Gordon Freeman becomes in the course of the game, it suddenly becomes not a mockery but an order. He's being told to not only rise from being thrust into the position of being just another oppressed citizen among many, treated by the Combine the same as any other under their subjugation, to the Combine's highest concern, Anticitizen One, The One Free Man more or less singlehandedly ruining their plans, and who eventually leads a ragtag human rebellion against the Combine. He quickly becomes a legendary hero and savior and beacon of hope. In other words... Rise and shine, Mister Freeman. Rise... and shine.
Also, you do rise to the top of the citadel, and make it shine with an explosion.
Alyx has a very improbable knack for finding Gordon. She does so in the beginning of Half-Life 2 just as Civil Protection start beating Gordon to death and later finds him in Anticitizen One with no explanation given other than a throwaway line (something like "I thought I'd find you here.") Considering the revelations we see in Episode Two it seems likely that a little birdie was whispering in her ear about where to find you.
Episode One begins with an Armor-Piercing Question from Dr. Breen: "Tell me, Dr. Freeman. If you can. You have destroyed so much. What is it exactly that you have created? Can you name even one thing?" ... and then immediately provides an answer, when the Vortigaunts (free to act on their own by Gordon's defeat of the Nihilanth) rescue Alyx from the Citadel collapse, and Freeman himself from the G-man's stasis. What has Gordon created? A future for an entire species (he's still working on attempt #2...)
When you leave the train station early in Half-Life 2, you can barely go anywhere before your way gets barred by a checkpoint. This is because you bypassed the usual entry procedures, thanks to Barney, and therefore don't have an access card (or whatever you use to get through the forcefields).
Ever wonder why there are so many puzzles involving the game physics and the Gravity Gun in-game? It's Freeman's area of expertise! He's physicist! Understanding stuff like that is his job!
In the first Half Life, you see a blue jumpsuit in Gordon Freeman's locker, likely given to him by Black Mesa. So guess what the standard issue of dress is for civilians in a world now ruled by the very same administrator as Black Mesa.
The Combine is a technologically advanced civilization which is inclined to spread its ideas of transhumanism and immortality to other worlds. They seem to believe honestly that it's cool to have your natural limbs replaced by "better" cyber-organic gadgets; after all, the Advisors are heavily modified, too. And they are willing to convince you of the superiority of their ways For Your Own Good, with military means, if necessary. So they invade Earth and, after an overwhelming blitz campaign, install a local government which shares their views on how things must be run and which is supported by a certain number of volunteers. However, they get stuck in a decade-long guerilla warfare against a rebel movement with its stubborn and backward prejudices. Those fanatics who send waves of barely armed infantrymen against armored units and reinforced positions (with respective losses) just don't catch that what they call genocide is merely collateral damage, a necessary bit of suffering and instability on the path to the bright future of humanity. And it has absolutely nothing to do with the fact that the Earth bears large amounts of a certain liquid resource which is very valuable to the Combine. This certainly rings some bells...
Throughout "Highway 17", you can see that the shoreline has gone out significantly, rendering docks useless and beaching numerous boats. Why? The Combine is draining Earth's oceans with teleporters. Considering how difficult water is to get in space and how essential it is for life, it make sense that the Combine has occupied Earth purely for this reason and isn't attempting to extract metals or other natural resources. Hence all the abandoned mines in the game (notably in Ravenholm and Episode 2).
At the beginning of Episode 1, Alyx says her father told her not to keep looking for Gordon, that he wasn't there; he's completely astonished when she finds him and checks in. The real reason he's so surprised? He knows about the G-Man, and knows that after the explosion, the G-Man would have put Gordon in stasis again.
The reason why the world was easily taken by the Combine in seven hours? The military exhausted all their resources fighting off the Xen creatures and the Race X. Thus the Combine saw an opportunity to take Earth, and the overwhelming force and technological superiority leads them to win the Seven Hour War.
Isaac Kleiner's name for his pet headcrab, Lamarr, seems random at first, until he mentions towards the end of the game that another name for her is "Hedy", meaning she's named after Hedy Lamarr, an actress from the 1930s to the 1950s. At first, it seems like a lame pun (Head-y Lamarr), but Hedy Lamarr was also a gifted mathematician responsible for co-inventing a method for frequency hopping and spread spectrum communication that's the precursor to Wi-Fi. Kleiner, being a scientist, probably held her in very high regard for this achievement, and named Lamarr in tribute to her scientific achievements (and partially for the pun).
During the beginning of the original game, the ambient chatter of Civil Protection officers and the Overwatch voice make frequent references to a "miscount", especially during the raid on the apartment block. They're actually talking about Gordon Freeman - when the G-Man puts him on the train there's one more person arriving in City 17 than there's supposed to be. As he walks around the train station and the plaza, they're trying to make sense of the anomaly, and finally track it down into the apartment block he's in. The raid is their attempt to pacify everyone so they can find the problem.
In Nova Prospekt, one of the things you hear the Overwatch voice say is "Attention Nova Prospekt internal containment team. De-service all political conscripts in block A7. Prohibit external contact." What do you find when you reach block A7? A dead vortigaunt. Clearly it was an instruction to kill it so it couldn't communicate with Freeman.
Much of the way the Overwatch voice speaks and some of the combine phrases are related to medical-sounding terms. Even when the topic at hand wouldn't normally be considered in such a way. Such has when you enter Nova Prospekt, the voice says "Possible Anticitizen One re-infection". This gets especially evident when they talk about non-sentient life-forms (which they refer to as "biotics"). They even refer to some combine squads as "stabilizers". It seems as if this is implying that the combine think of other lifeforms as a virus or bacteria that must be contained, and any non-compliant lifeforms are inflicting and infecting "wounds" to the combine operation. Those wounds then need to be treated or "stabilized" by getting rid of the infectant.
Perhaps most telling is a radio message referring to Freeman as "Status: Malignant". In a way, that makes perfect sense: Freeman's growing reputation, and hence his growing number of followers and rebels, is seen like a spreading cancer.
In the original game, Freeman is exempt from the one hit kill attacks from Combine sniper rifles and disintegration balls that every other NPC is subject to, instead only taking 20 damage from each attack, barely 10% of his full health. The Overwatch Pulse Rifle deals a mere 3 damage when used against him, while it deals 8 damage to anyone or anything else. Also, the anti-personnel guns on the Strider and Gunship deal surprisingly little damage to Gordon for the autocannon equivalents they're supposed to be. What do well these weapons have in common? They're all Combine dark energy weapons that don't work like Earth firearms. Kleiner did say he upgraded Freeman's HEV suit- of course he'd do whatever he can to make it specially resistant against Combine weaponry, which wasn't known to exist at the time of the HEV suit's construction.
In Half-Life 1, the various NPC scientists will occasionally say something about the mathematical improbability of a resonance cascade, or that the odds of such an accident happening were astronomical. At first this just seems like idle chatter. Then we get to this game, and it turns out they were right - it WASN'T an accident, but a deliberate plot by the G-Man and Dr. Breen.
One of the rebels who you first encounter, and who is severely injured, is named Winston. Winston Smith is the protagonist in the novel 1984, which inspired City 17's harsh brutality of civilians, and heavy surveillance.
Back in Half-Life 1, the running animation for the Vortigaunts appeared somewhat unusual, almost silly, as they appeared as if they were attempting to skip around. What may seem to be bad animation actually seems quite brilliant when you consider that the Vortigaunts are from Xen, where the gravity is much lower. The Vortigaunts must be quite used to moon-skipping around to travel from place to place quickly on Xen and by instinct, they move the same way on Earth, although with less satisfactory results. By extension, one could imagine the Vortigaunts are commonly used to jumping, knowing all the platforming that is required to even maneuver around in Xen. Those goat legs are probably great for that.
Taking this one step further, in this game, the Vortigaunts tend to move relatively slowly compared to human NPCs, even while apparently sprinting. Once again, they retain a large bounce in their step, but they seem to shuffle about uneasily and cautiously. This may seem tedious, but again, you have to take into account that these creatures were likely born/created on Xen, where their bones & muscles (or whatever alien equivalents) are used to much less stress than they receive on Earth, thus they have more trouble moving around on Earth.
Uniting these two points, there is a great explanation as to why the running animation is slightly different between the two games, besides technological upgrades. The Vorts in Half-Life had just been popped onto Earth for the first time when you encounter them, and have only been on the planet under the span of a few hours at maximum (most commonly, you meet them just as they get dropped into your planet) and thus, they have not had the time to adjust. Meanwhile, the Vortigaunts in 2, most likely having been on Earth for a period of years, have adjusted and don't skip so strongly anymore, yet they still retain some of their walking pattern, seeing as evolutionary traits are hard to shake. These Earthly Vorts have been under the strain of Earth gravity for an extended period of time, and thus, have lost their strength to hop around so freely, nor do they bother to muster it up. Also, potentially worse living conditions on an alien planet (as opposed to when they worked under an empire on their home planet) probably has been very detrimental to their health, so they don't have the strength to hop around like they did on Xen.
G-Man often addresses Gordon as if he worked for G-Man, meaning when Gordon was taken out of G-Man's influence at the beginning of Episode 1, he was given a mandatory reprieve.
This one is about the "Epistle 3" plot summary that's been making the rounds. Half-Life 1 and 2 both ended with the G-Man putting Gordon in stasis, taking him out of the action so he doesn't know how things actually turned out. The Vortigaunts' intervention is the only reason he's able to stay in the Half-Life 2 setting for the Episodes. The fact that he stays in that setting for a direct continuation of the second game is why the episodes aren't called Half-Life 3 Episode whatever, despite taking place after 2. An ending to Episode 3 that took Gordon out of the conflict with the Combine would presumably lead to an actual Half-Life 3 which was about an entirely different conflict. That might even be why the series is called Half-Life: Gordon keeps leading "half-lives" as he fights different battles but never gets to actually finish things.
Alien species such as Bullsquids, Houndeyes, Gonomes, and most Ichthyosaur (You only see a grand total of one in a cutscene in the sequels) are all missing after this game.
Gonomes looked like an advanced stage for Headcrab Zombie victims, with the Headcrab mutating their host to be bigger, tougher and practically fused to their Headcrab. Combine are seen using Headcrabs as a form of biological warfare, seemingly splicing up new species of Headcrabs in the process. If Headcrabs really were domesticated for use in warfare, then it wouldn't be too far off to assume that the Combine's meddling in Headcrab genes either phased out the later stages in their life cycles, or that their artificial species simply can't advance past a certain stage of infection. That, or all the zombie-infested areas you visit just weren't allowed to fester long enough for you to see any advanced phases that leads to victims becoming the Gonome (though this one delves into Fridge Logic since Gonomes were encounter in roughly a day or so into the Black Mesa Incident.)
Ichthyosaur have to compete with / survive against Leeches in the water and especially ocean, who were noted to have utterly consumed most species of life in the water. It may be why you only see one in what looks like a lake, in what may be one of the few bodies of water not decimated by Leeches and thus would sustain at least some life, enough to at least keep an Ichthyosaur alive.
One of the quotes you can hear the citizens saying is "Sometimes, I dream about cheese." This seems random at first but considering the setting of the game, it is unlikely citizens are able to get cheese, or any kind of remotely tasty food for that matter hence cheese haunting their dreams.
It stands to reason that the Hunters are weak to strong, physical impacts. Those skinny legs cannot hold so much weight upon them for long.
During the Train Station Finale in Episode 1, you fight a unit of Civil Protection instead of regular Combine soldiers. Why? They probably defected from the Combine and are trying to steal a train for themselves before the rebels seize it or the Combine destroys it. This also raises interesting questions about how former Civil Protection officers would be treated in a world where the rebellion is victorious, as Episode 2 implies it is coming close to be.
Throughout Highway 17, Sandtraps and Episode 2, you can see several functioning and abandoned rebel bases outside of City 17, the implication being that, unlike City 17, which is a tightly controlled police state, the Combine's control of the countryside is far more loose. According to the history of guerilla warfare, urban populations are far easier to control than rural ones. Essentially the countryside is in a constant state of guerilla warfare which residents of City 17 may not even be aware of.
Gordon not being able to control the Antlions in the Episodes can be explained by him losing the Antlion bugbait back in the Confiscation Chamber at the climax of the original HL2.
The G-Man really is kind of a jerk. Considering the creepy obsession he has with Alyx Vance, it's safe to say that he made sure she's stay alive through the events of the first game since she was at Black Mesa at the time... but he didn't let her mother live, which may be the "high cost" for "plucking [Alyx] from Black Mesa" he mentioned.
Speaking of G-Man, remember how he banished Adrian Shepard into Xen because he knew too much? Well, at the end of Blue Shift, Barney manages to escape with several other scientists... who are never seen or heard from again in 2. They probably either got killed by the Combine or the G-Man thought they knew too much as well, and gave them a free pass to Xen as well.
And nobody knows what happened to Dr. Gina Cross or Dr. Collette Green, nor the disabled Dr. Keller who helped them. In one of the locations on Xen that you can teleport to with the Displacer gun's alternate trigger, there's a flooded cave filled with dead scientists, and one of them looks awfully like Dr. Green in her red HEV suit.
At the beginning of the chapter "Entanglement", Alyx says an occasional Vortigaunt has been captured and sent back information about Nova Prospekt. In the previous level, you see a Vortigaunt in a torture chair, dead.
It's entirely possible that Gordon, as well as Alyx, is being fed hypnotic suggestions during his journey. Think back to that TV set with the G-Man on it, broadcasting that weird music - harmless little G-Prank, or a trigger meant to bend Gordon to the G-Man's will? It's entirely possible the G-Man had time to perform experiments on the poor dude while he was in stasis for ~20 years.
When you look over Alyx once she's been stabbed by the Hunter, you'll notice two things: her eyes are half open, but not tracking, and she's certainly not breathing in any visually detectable way. She's probably already dead, but dead for a short enough period that the Vortigaunts can keep her from passing on completely, and even bring her back. Which also makes the Vortigaunts even more intimidating.
It's probably due to the Vortigaunts having a close relationship with electricity; in theory, they could be externally pacing Alyx's heart to maintain her circulation — machines exist today which do this, so it's not too much of a stretch to imagine Vortigaunts doing it, too. This also implies they're doing something else, not made obvious to the player, to oxygenate her blood, without which pacing would be pointless. It also implies her heart has actually stopped pumping blood on its own, which isn't implied by an absence of respiration, but the game's lack of a "check pulse" button makes it difficult to tell.
And of greater importance than all of the above, would be that the Vortigaunts do something about the two through-and-through stab wounds in Alyx's abdomen. Such injuries are often survivable, but only with immediate surgery to repair bowel perforations and close the wounds; this assumes no damage to major vessels, such as the abdominal aorta, as such damage tends to result in very rapidly fatal exsanguination (i.e., bleeding to death). One assumes the Vortigaunts have already tended these wounds; otherwise, cardiopulmonary maintenance wouldn't be worth much, as it's hard to perfuse a patient who's leaking out both sides of her belly.
A scrapped concept from the original Half-Life has the Vortigaunts using their powers to revive dead Vortigaunts.
Besides the drain on the world's resources by the Combine, something which was even toned down from miles upon miles of dead earth in the beta/leak, there's also insane amounts of irradiated water and waste filling up entire canals and areas as Gordon rides around on the airboat. The HEV Suit protects him, sure, but what about all the rebels and their stations that are built around these radiated materials? They wear nothing but civvies or stolen vests and clothing, and the very person who prepares the airboat for you is just in an open end of the canal, on some wood boards inches above entire waist-deep pools of the stuff.
Most of the characters you meet during the game seem to be around the same age, give or take a few years, probably between 20 and 30 (we'll say 25 for argument's sake). Given that almost 20 years have passed since the first game, that would put most of the people the player encounters at the age of 5 when the events of 'Half Life 1' occurred. That game was scary enough for an adult to experience, imagine being a child and waking up one day to find that mummy and daddy have been turned into slobbering zombies with their guts hanging out, your small town is in the process of being obliterated by alien war-ships and the marines are gunning down anything that doesn't look human.
Unless there's another way we may not know, it's not possible to revive Eli Vance with the same method used to revive Alyx earlier in Episode 2, because the Antlion Guard who guarded the nest was killed after Gordon, Alyx and the Vortigaunts escaped from the mine and even if it wasn't, there's the fact that Eli got his brains sucked out by the Advisor, whilst Alyx was just in a near-death state. So, from now on, All Deaths Final.
In Half-Life 1 it is mentioned the the military is tracking Gordon through his HEV suit. Could the Combine possibly be doing the same, hence enabling them to set up roadblocks and ambushes for Gordon in Highway 17? If this is true, then it means that Gordon was responsible for the destruction of the Railroad, a network to help refugees escape City 17. As well as the raid on Black Mesa East which captured Eli Vance.
Throughout Ravenholm, you can find several Combine rocket shells that they had used to take out a Railroad station in Route Kanal. This strongly implies that Ravenholm was destroyed by the Combine long after the Seven Hour War. Considering the proximity to Black Mesa East, it was probably a safe haven for refugees, until the Combine turned it into a living nightmare.
While Barney's comment about being "behind on his beating quota" is probably a joke, it does beg the question of what he is having to do in order to maintain his Civil Protection cover.
It is shown throughtout the game that the Combine holds Nova Prospekt prisoners in stasis in coffin-sized containers which also keeps them restrained. The same sorta containers exist in the Citadel. In total, the number of those prisoners may be in the thousands. Gordon was responsible for blowing up both Nova Prospekt and the Citadel.
It gets worse: in Episode 1, those containers are shown falling into the chasm from a broken conveyor. Imagine this: you are restrained by a metal straight jacket in a coffin-sized container and the conveyor transporting you breaks off over a chasm. And there is nothing you can do but watch.
It seems many of the coffins are empty given that there is an entire line of them used in the Citadel that are empty. However, if you played that part, you'll notice half of them go off to reconnect with the line and the other half goes and gets hit by an electrical arc. Now, unless that sterilizes the things or somehow fixes them, that probably means half the people on that track end up dead. If you are on the other side of the track, you get to see someone get roosted.
Gordon Freeman is also (albeit indirectly) pretty much the reason Alyx's mother and father both died. He triggered the Black Mesa incident and was the reason the Combine managed to track down the White Forest base. Barney cracking jokes about Gordon getting followed don't sound so funny now, huh?
Freeman is also directly responsible for the Combine's clampdown on the underground railroad in City 17; he basically led them straight into it on his flight to Black Mesa East.
His thesis is "Observation of Einstein-Podolsky-Rosen Entanglement on Supraquantum Structures by Induction Through Nonlinear Transuranic Crystal of Extremely Long Wavelength (ELW) Pulse from Mode-Locked Source Array". Which means he might have started the trend of shooting alien crystals with lasers.
Humans haven't been able to reproduce for around twenty years. Now add to that all those who were killed when the Combine invaded, those who were made into Soldiers or Stalkers, those killed during skirmishes or else have fallen prey to the numerousotheraliens, and those blown up in Nova Prospect/the Citadel. The end result? That humanity is steadily marching towards extinction.
At the end of Episode 2, though, the suppression field is disabled, and the Combine are cut off from their commanders.
Also, most of the rebels you see throughout the game look quite young - a lot of them would have been children during the Seven Hour War and have never lived a life free from the Combine.
In Episode 1, you are introduced to the Zombine, a Combine transformed into a zombie. You can still hear the cries of the zombie through the soldier's vocoder. On closer inspection, you can hear that the soldier is still conscious, and you hear him attempting to warn his allies that there are zombies in the area. Imagine being a soldier listening to your zombified allies attempting to warn you over the radio.
One of the Combine's lesser security measures is a force field that only lets recognized individuals pass through - so to Gordon, they're a solid wall. In a few places, force fields are used to block off train tracks to stop the player wandering the wrong way. Both Combine and human trains are repeatedly seen passing through these force fields. Have fun thinking about the passengers who were randomly reassigned anticitizen status mid-journey!
Though, the shield could be disrupted or turned off by the presence of the train. If the force field uses electricity in some way, electromagnets may keep everyone in side safe (why make a mess of the train when you can just screw the passenger over when s/he gets to the next stop?)
In the first game's Scenic Tour Level, you can mess with a microwave and destroy another scientists' lunch. This is played for laughs and only brought up again when you meet Magnusson in Episode 2, who's annoyed about it. But consider it from his point of view: About 20 minutes after you wreck his lunch, Gordon triggers the resonance cascade which forces Magnusson and everyone else to flee, and the 7 hour war later that very day brings all of humanity to its knees. Magnusson's probably been scrabbling and scavenging for years, living off of canned goods or military prepared meals. Gordon may have ruined Magnusson's last chance at a decent meal in his entire life. And even if Freeman doesn't ruin the casserole directly, when you get back it doesn't look particularly appetizing. It could be that even if Freeman's fiddling with the microwave didn't ruin Magnusson's lunch, the disaster did. In which case, Freeman was at least partly responsible. Double horror if that was made for Magnusson by his wife.
In the beginning of Half-Life, after you get the HEV suit, you can open Gordon's locker. Inside is a picture of a baby, probably Gordon's. That means Gordon had a family, who are probably dead now.
Gordon may also have had parents, aunts, uncles, siblings, cousins, grandparents, etc. All of which could be dead or not locatable. This is happening to EVERYBODY.
In Civil Protection, it is mentioned that the language on the walls gives away where City 17 is at. They are some place in Europe in a country that was formerly part of the Soviet-Union. The Combine seems bent on oppressing the human population, so what better way to do that than shuffle us all around the planet, displacing everyone from their homes and taking them to places where the signs on the buildings aren't even written in a familiar alphabet? Granted, it would be better to shuffle people around at random, using a mix of languages as a barrier to uprising, but hey, the combine put loud, audible EKG meters and glowing eyes on their soldiers' uniforms, so they are just a bit stupid.
The inefficiencies in population-shuffling WOULD give a nice non-G-Man-related reason for why so many major characters wound up in the same region, though.
Alternatively; the combine HAD to keep all the citizens speaking the same language so their thought police could order them about without being misunderstood.
When you think about just how risky Freeman's actions really were. The Combine vastly outmatch the human forces (what they'd left on Earth was a skeleton garrison to keep order - the super-portal shows that they could have easily overwhelmed us if they wanted to) and were only keeping humanity alive to test out how useful we might be to their empire. Then Freeman arrives and kills scores of transhuman troops (effectively showing how useless they are), blows up their synths and installations, and pretty much demonstrates to them that humans are more trouble than they're worth. Had he not managed to infiltrate and disable the Citadel, and then successfully find and deliver the codes necessary to destroy the super-portal, the whole human race would most likely have been exterminated. Thinking about it like that, Breen's attempts to stop Freeman and appease the Combine make rather more sense.
This could go one of two ways in the long run; someone like Gordon could easily of just doomed all of humanity to be exterminated once the Combine can move in full, or his survival and combat capabilities and the sheer amount of destruction that follows in his wake may have other consequences. If G-Man, who is Ambiguously Human enough as it is, had Freeman's contract 'open to the highest bidder', imagine how terrified or impressed the Combine might be at the idea that one man of this puny species basically caused a planet-wide rebellion. Especially if they could've had him on their side.
Remember the Nihilanth? The final boss of the original Half-Life? He had personal combat abilities that would at least let him take on an entire platoon of soldiers (and indeed, he can if you decide to open the console and spawn some in his room or spawn him near some soldiers), and psychic powers that can affect things on a planetary scale. It was him and him alone who telepathically controlled the Vortigaunts, kept the dimensional rift open, and caused the devastating portal storms around Earth. Here's the kicker: according to Word of God, the Nihilanth's "I am the last" comment was referring to the fact that the rest of his species was hunted down by the Combine. Imagine millions or, more likely, billions of beings on par with the Nihilanth (likely stronger actually, since the Nihilanth himself had not only been injured previously, but was expending most of his powers bringing an entire army to Earth and holding the rift open). These guys were hunted to extinction by the Combine, to the point where their last survivor was willing to jump into Earth solely because the Combine couldn't get there. The Combine seem a lot scarier now, huh?
And don't forget his even more disturbing quotes such as, "We are their slaves" and "He is not man"/"He waits". Just tragic.
Also according to Word of God, Eli lost his leg to a Bullsquid while trying to get Kleiner over some sort of fence. He also lost his wife, his entire life save for one picture, and considering it was G-Man who actually saved Alyx for the sake of speculation let's just say he probably didn't know where his daughter was. Just got half-eaten by an alien and your whole world will be gone in a matter of hours. And that's just the one person's backstory the community knows in whole, imagine everyone else!
If you look hard enough around the gas station in the chapter Highway 17, there's a citizen who shot himself with a magnum that you can pick up. Now think of the implications of why he shot himself.
The nazis dominated most of Europe within a few years. The Combine dominated the entire Earth within 7 hours.