The following is from a post by member "Cardboard Box A" on the SomethingAwful.com forums:

Okay, so here are answers to many of the common questions:

First things first,

This Book on the making of Half-Life 2 answers a LOT of questions. A lot of the answers mentioned here are excerpted from this book.

How long has it been since the first game?

The book says 10 years.

Where the hell does this game take place? Where is City 17 located?

One thing Valve has mentioned time and time again, and yes, in the book as well, is that City 17 is supposed to be a nondescript Eastern European city. Architecturally it looks like one, and much of the writing is in Cryllic. Valve liked this setting because it exemplified the theme of old versus new and the cost of technological change that is featured in the game (the shining new Combine structures and technology set against an old world backdrop).

Some have speculated that it was probably a "Science City", a cold war relic from the days of the USSR, a settlement that sprang up around research facilities that the Soviets set up. If you think about it, Black Mesa was also a cold war relic (missile base converted into research facility), so it makes sense that Valve would feature a parallel like this.

The City is filled with Americans and former Black Mesa personel because, well, it's one of the few population centers left in the world that people can relocate to. Why is the world like this? Read on:

What the hell happened after Half-Life to make the world this way?

Read this, it's an excerpt from the book that tells the backstory Valve was planning to include but didn't. Basically killing Nihilanth didn't end things, portals continued to open up all over the planet and all of the hostile Xen creatures ran rampant, making the world unsafe. The survivors flocked to population centers that were easily defensible against the Xen wildlife. However, sometime after that, the mysterious Combine simply teleported into the middle of each population center with their giant towers and incredible military might. What was left of earth's forces didn't stand much of a chance, and as you can see from bulletin board clippings in Eli's Lab in the game, it was over in 7 hours. Somehow, the mysterious Dr. Breen, the former administrator of Black Mesa, showed up and somehow negotiated humanity's surrender to the Combine. Apparently he promised humanity's cooperation (willing or not), subjects for experimentation, and access to earth technology.

Who are the Combine? What do they want? Why are they here?

According to the book, Valve envisioned the Combine as the ultimate Interdimensional Borg-like threat. They invade and enslave other worlds they consider advanced enough to pose a threat and add their biological and technological distinctiveness to their own. For example, the Striders and Gunships and similar ships seen inside the Citadel are from a race known as the synth, a self-adapting bio-technological robotic race (think cyborg replicators), that the combine conquered sometime in the past.

It is likely that humanity added themselves to the "watch" list once they proved themselves capable of interdimensional travel and to the "imminent threat" list with their hostile takeover of the border world, Xen. Some theorize that the Combine themselves were the ones in control of Xen, and that humanity's incursion into what was essentially their territory is what prompted the invasion of earth. This is also plausible.

Their interest lies in conquering humanity to make sure that they are no longer a threat to the rest of the multiverse and themselves and acquiring humans as potential members and forces (note most of the Combine troops you face in the game are in fact humans) and acquiring advanced human technology and weapons (which, if you think about it, are pretty advanced in terms of local teleportation technology and weapons like the Tau Canon and Gravity Gun). Essentially, they want to draft humanity into their ranks and pacify those who don't want to join. Also, they are either draining earth of it's natural resources or converting it into another home for themselves or perhaps both at once.

What is Administrator Breen doing working for the Combine?

Based on what we hear from him in the game, he does seem genuinely concerned about humanity and it's future, and wants us to survive, even if it means joining the Combine. Breen seems especially concerned about the performance of his Combine soldiers when he addresses them regarding their inability to stop Gordon Freeman ("he is not an assassin, he is a theoretical physicist!"). It is plausible he fears humanity's future is at stake if our performance is not satisfactory to the Combine masters ("Our Benefactors"). It is likely that in negotiating Earth's surrender he made certain promises to secure humanity's future, and keeping those promises is important. If he can't put down the resistance, then perhaps the Combine will conclude humanity is too great a threat to be pacified and must be eliminated?

Also, The picture seen spraypainted on the wall in a couple of places appears to depict the Combine as the future evolution of man, as above our current state as we are above apes. This seems to tie into all of Breen's talk about "improving" humanity and "immortality being right around the corner", perhaps he is finally in the position of power he always wanted to be in? There are conspiracy theories surrounding Breen's role in the whole saga, remember, in the first game "The Administrator insisted that we go ahead with the experiment" and "The Administrator went through a lot of trouble to secure a sample this pure" - the same sample that set off the resonance cascade. Perhaps he has had a bigger role in all of this than he lets on? One thing is clear - there is no way that the former Administrator of Black Mesa being made the Administrator of earth itself under Combine rule is a coincidence...

Here are some of his quotes from the game, courtesy of the Steampowered forums

"How could one man have slipped through your forces fingers - time and time again? How is it possible? This is not some agent provocatuer or highly trained assasin we are discussing - Gordon Freeman is a theorhetical physicist who had hardly earned his PHD at the time of the Black Mesa incident. I have good reason to believe that in the intervenig years we was in a state the precluded further developement of covert skills. The man you have consitently failed to slow, let alone capture, is by all standards simply an ordinary man. How could you have failed to apprehend him?"

"Well, I will leave upbraiding(?) for another time to the extent it proves necessary. Now is the moment to redeem yourselves. If the trans-human forces are to prove themselves an indespencible augmentation to the Combine Overwatch, they will have to earn the privilage. I'm sure I don't have to remind you that hte alternative - if you can call it that - is total extinction. In union with all the other unworthy branches of the species."

"Let's not allow it to come to that...I have done my best to convince Our Benefactors you are the finest the species has to offer. So far they have accepted my argument. But without concrete evidence to back it up, my words sound increasingly hollow, even to me. The burden of proof is on you - as is the consquence of failure. Just leave it at that."

Breen quotes from inside the Citadel:

"It's ME you should be concerned about. I can still deliver Earth, but not without your help!"

"Having both of you in my keeping ensures I can dictate the terms of any bargain I care to make with the Combine."

"I agree; its a total waste. Fortunately, the resistance has shown it is willing to accept a new leader. And this one has proven to be a fine pawn for those who control him."

What were those weird things I saw inside the Citadel?

Those biological ships that looked similar to the Striders and such, as mentioned above and in the book, were from the synth, a bio-technological race that the Combine conquered previously. They were engineered into living weapons. Those crab-like walking things were crab-synths (no really) which didn't make it into the game as an enemy. The other ships and such are just other "models" of synth that, again, you don't end up fighting.

Those creepy gaunt humanoid creatures with metal faces are in fact former humans who have been experimented upon. Remember Nova Prospekt? The enemies of the state are taken there to be subject to inhuman experimentation. Apparently they are lobotomized and many organs are removed so that they are reliant upon direct intravenous feeding for sustenance, and then are shipped to the Citadel to serve as mindless drones for menial labor. The book mentions that Valve had originally planned to make them enemies that you fought (remember the red laser eye thing?) but would feel really bad about, but decided against it for some reason.

What is that slug thing Breen talks to on the viewscreen?

In the book Gabe talks about how Valve imagined the originators of the Combine as being a race that evolved to depend on technology so much that their bodies atrophied to the point that they were basically limbless slugs, but extremely advanced in intelligence and reasoning, allowing them to be very adept at manipulating and controlling everyone else.

Why do the Combine use headcrab shells? They don't like headcrabs or headcrab zombies...

They use them as inexpensive and effective area denial biological weapons. Human resistance fighters are smart and a formidable threat, they can plot, they can infiltrate, they can organize and coordinate, and they can use devastating weapons. Headcrab zombies are none of those things and nothing more than canon fodder. If you think about it, it's pretty simple, just let headcrabs loose, they are sneaky and tenacious predators, they will get into vents and hide in cielings and they will get onto people's heads. Once they turn into zombies they begin to indiscriminately kill any other resistance members that might be alive. They are a very serious threat.

It is likely that the different varieties of headcrabs and headcrab zombies come from the Combine experimenting with them genetically and attempting to engineer a better biological weapon, hence the spider and neurotoxin varieties. Also, it's worth considering that headcrabs were nothing more than biological weapons intended for use on humanoid enemies all along. If you think about it, their primary function is to latch onto enemy heads and turn them into mindless berserkers intent on killing even more enemies. It's a very smart design, every headcrab is capable of disabling one enemy and crippling or killing dozens more from the inside. Xen was no stranger to biological weapons, remember the snarks and the bee-gun?

Also, the book mentions how Gonarch and it's tiny spider babies that you fought in Xen in the first game were supposed to be the headcrab queen and baby headcrabs, respectively, but that they hadn't thought through the headcrab life cycle completely at the time. Therefore any inconsistencies between the first game and the second with regard to the headcrab life cycle can be chalked up to a bit of revisionism on their part.

Why the hell are those Vortigaunt creatures on our side now?

They were just slaves forced to fight in the first Half-Life, they weren't actually hostile. If you paid attention, they were refered to as "alien_slaves" or somesuch and wore slave collars around their necks, which they no longer do in HL2. Also, when you see them in the factory on Xen, they are not hostile at first, and only begin attacking once the Alien Controllers (the flying fireball throwing guys) show up.

Killing Nihilanth freed them, and if you talk to them in Half-Life 2, you will note that they are eternally grateful to "the Freeman". Of course, now they are just under the tyranny of the Combine.

They also talk about how that "now that the lesser master is gone, the greater is sure to fall as well". This implies that even Nihilanth had a boss to answer to. If you notice, even Nihilanth was wearing a slave collar in Half-Life, and one of the things he says is "slaves, we are all their slaves". Some theorize that this may refer to the Combine, who might have been the ones in control of Xen. This is certainly plausible, and there does seem to be one possible connection - the metal "thingy" that Nihilanth floats on top of in the original HL (noclip to get a good look) appears to be VERY similar in design to the metal "thingies" you see attatched to the various synth ships inside the citadel.

Do the Vortigaunt know about the mysterious "G-Man"?

If you talk to them, they will often say that "we both serve the same mystery" (their mastery of english is hardly complete). One of them in the canals even has the G-Man on the television and says that line to you as he changes the channel.

Here are some of the things the Vortigaunts say if you keep talking to them in HL2, courtesy of the Steampowered Forums:

"That sharp spur of hope has not dulled to this day. For once the lesser master lay defeated, we knew the greater must also fall in time"
"Your bright face obscurs your darker mask"
"Could you but see the eyes inside your own, the minds in your mind, you would see how much we share"
"How many are there in you? Whos hopes and dreams do you encompass?"
"We are you, Freeman. And you are us"
"We never dreamed to meet you in corporeal form"
"There is more to the Free man than meets the eye"
"We call you sib, although your mind and meaning are a mystery to us"
"Far distance eyes look out through yours"
"Something secret steers us both. We shall not name it"
"We will put aside Black Mesa, for now"
"Your mind is opaque"
"We are a tapestry wovened of vortessence, it is the same for you if only you would see it"
"There is no distance between us. No false veils of space or time can intervene"
"We serve the same mystery"
"Our purpose is mutual"
"There is no distance between us"
"While our own lay scatter at your feet, you severed the vortal cord that bound the Nihilanth to life, and to us"
"We see you still in Black Mesa, clearly we see you in the Nihilanth's chamber"
"We bare witness to the bright eternity of the Nihilanth's demise. You leap, you fall, we see you flash between the barriers"
"For a brief time you joined us. You are one. Between the worlds"
"Communion of the vortessence. And that other; a deeper mystery. No deeper than the void itself"
"We cannot forget those whos cords you cut. Forgiveness is not ours to bestow"
"Unity of purpose, the shattering of common shackles, a single road we tread"
"You have brought us grief and jubilation beyond mesaure"
"We are there still in observeance of your final stroke"
"With you besides us, a tailsman of victory, the day of freedom draws nigh"
"The way ahead is dark for the moment"
"What seems to you a sacrifice is merely to us an oscillation; we do not fear the interval of darkness"
"We remember the Freeman, we are coterminous"

Who is the mysterious "G-Man"? Is he human? Alien? What is he up to? Is he "pimping" Gordon out?

The book mentions that he has trouble pronouncing his words, as if he is not quite used to human speech. This pretty much spells out that he is NOT human. He looks human, however... given Breen's conversation at the end of the game, it would appear that the technology to transfer a being's "conciousness" or mind into a different body exists. Could the G-Man be using something like this? We don't know for sure.

In the first game, he appeared to be a shadowy Agent of the US Government (hence the "G-Man" or "Government Man" monkier, which is also the name of his multiplayer model, "GMAN") in the first game, backed up by his briefcase, his pleasure at the fact that the US Government troops were successful at conquering Xen, and his confiscation of Gordon's weapons on the justification that they were "government property after all". Since the US Government no longer exists in the world of Half-Life 2, it is unclear what his role is now.

He seems to possesses the ability to appear anywhere he needs to be, as well as the ability to teleport anyone he wants between dimensions as well as into a stasis holding dimension of sorts. Indeed, he has a great deal of power... but he doesn't seem to intervene directly in things. Instead he others to accomplish his goals...

It is clear that he is using Gordon's extraordinary fighting skills in order to take down enemies of his at whatever opportunity he sees fit. He knew of Nihilanth and Xen in the first game and Gordon got it done. In HL2 he knows of Breen and the Combine and Gordon, well, gets it done, killing Breen, cripping the earth operations of the Combine, and destroying their means to easily teleport into our dimension. Breen also mentions that Gordon is just being sold to the highest bidder... however, the G-Man himself says that while he has gotten offers, he has NOT entertained the thought of going mercenary with Gordon YET. To some degree we can't really trust either of them, but the G-Man has been pretty honest about things so far, as he doesn't really need to lie, just to be really vague. Also, if we consider Opposing Force to be canon (see below regarding that issue), it would seem that the G-Man is building up his forces of extraordinary individuals with incredible survival instincts and combat skills... Gordon is just one of several agents he may intend to use for his purposes.

As for the theory of G-Man being Gordon Freeman from the future... yes, well it's true they both have sparkling green eyes (based on the box art) and somewhat similar (though NOT identical) facial features... but it would be unlikely for Livestock's joke review posted on the SA front page to be right... I don't think anyone really expects writer Mark Laidlaw to go down this route.

Okay, so what about Opposing Force and Blue Shift? Where's Col. Shepherd?

Valve hasn't given a definitive answer on this but it is likely they are not strictly Half-Life canon. Valve is free to ignore or incorporate elements of the stories of both expansions, we will have to wait and see what they do.

What the hell happened in Opposing Force and Blue Shift anyway? I didn't play them...

In Opposing Force you play Cpl. Shepherd, one of the marines sent to kill aliens and stop Freeman. You don't, of course. It covers what happens at Black Mesa after Gordon travels to Xen (spoilers for OpForce) Another alien force, known only as "Race X", decides to take advantage of the dimensional instability and invade Black Mesa. Shepherd beats them back and kills their giant monster leader, presumably thwarting the invasion. Meanwhile the Black Ops and the G-Man nuke the entire facility. G-Man treats Shepherd much as he did Gordon, putting him in dimensional stasis of sorts until he needs him again. Again, Valve may not consider this canon.

In Blue Shift you play Calhoun, one of the security guards caught up in the events, he helps a few of the scientists successfully escape from the facility. It features the only happy ending of anything Half-Life related. It also shows how humans had to set up a relay station in Xen itself in order to enable local teleportation on earth.

But did Alyx really die? What about everyone else? How could they survive that explosion?

We simply don't know. The game ends before settling any of these issues. Yes, from the last vantage point, it seems unlikely that Alex could have survived the dark matter cataclysm... however, Valve did invest a lot of effort into her character, and they have said that they intend to release mini-expansion packs or at least levels featuring her over Steam, so... it's not in their interest to kill her off. So, yeah, up in the air.

It's plausible that the other characters were far enough away from the explosion to survive. At this point Valve is free to bring anyone they want to back.

So what happened to all these weapons and levels and enemies that we saw in the videos and the leak and read about?

Simply, they were cut. Most of the levels still exist in some reworked form, traptown is in Ravenholm, but there are no Combine there, for example.

Some enemies were reworked as well, for example, the book talks about how the original Combine Assassin that you see in concept art was made into the Advanced Guard that you see in the Citadel. The berserker, originally a combine experiment, was reworked into the fast headcrab zombie. The book also talks about how the really cool water tentacle enemy was cut simply because as cool as it was to watch, it just wasn't any fun to fight against. It is likely the portion of the game that featured the water tentacle was cut along with it. Who knows why the bullsquid and icthyosaur were cut, or where the houndeyes are now.

As for weapons, well, who knows exactly why they were cut. Valve seems to have wanted to cut down on the variety of weapons in the game, perhaps to focus on the primacy of the Gravity Gun. The OICW was probably cut since the whole OCIW program was scrapped in real life. Other weapons like the sticky bomb launcher and the physics manipulator (blue beam in the physics demonstration movie) never made it past the prototypical stage.

What are some things said by important characters in the previous games?

From the Steampowered forums:

Nihilanth:

"Alone.. not you, alone.. not you, alone." - Can't make heads or tails of what this means "Comes another..." - Another person comes to Xen
"Deceive you.. will deceive you" - Could either be that someone is going to deceive Freeman or Freeman will decieve someone else. Possibly the Gman will deceive him, or Dr. Breen?
"Die, you all die, you all die." - Either every human who's come to Xen so far has died there, or he is just saying something like 'I hope you all die' or something.
"Done... what have you done?" - After you kill Gonarch (the giant headcrab mother).
"Freeeeemaaannnn!" - When you enter his lair and are face to face with him
"The last... you are the last... you are..." - Probably the last problem to be dealt with, I would say the last person to come to Xen but Shepherd went there a little while after Freeman did.
"You are man... he's not man... for you he waits.. for you..." - Referring to the Gman, who's waiting for you after you beat Nihilanth.
"Now die, now die.. now..!" - After he sends you to a room with a Gargantua on the land and an Ichyosaur in the water to kill you.
"Their slaves.. we are their slaves.. we are..." - Pretty self-explanatory, slaves to someone, possibly the Combine, or Race X.
"The last... I am the last!" - Last obstacle in the game, really. Maybe some deeper meaning.
"The truth.. you can never know the truth." - Interesting, I think it may have something to do with Breen, and the teleportation experiments, and the whole story of it all, really. Too complex or summat.
"Thieves, you all are thieves, you all are..." - Because you took the crystals from Xen, referring to the Black Mesa researchers in general for taking them for their own purposes.
"Win, you cannot win.." - Just saying you can't beat him, probably.

Gman in Half-Life:

"Gordon Freeman, in the flesh, or rather.. in the Hazard Suit. I took the liberty of relieving you of your weapons, most of them were government property... as for the suit... I think you've earned it."
"The Border World, Xen, is in our control, for the time being, thanks to you... quite a nasty piece of work you managed over there, I am impressssssed."
"That's why I'm here Mr. Freeman, I have recommended your services to my eh-eh-eh-eh-eh-employers and they have authorised me to offer you a job! They agree with me that you have limitlesssssss potentiallll."
"You've proved yourself a decisive man so I don't expect you'll have any trouble deciding what to do, if you're interested, just step into the portal and I will take that as a yesssssss..."
"Otherwise.. well, I can offer you a battle you have no chance of winning.. rather an anticlimax after what you've just survived."
"Time to choose..."
"It's time to choose.."
[If you choose to work for him] "Wisely done, Mr. Freeman! I will see you up ahead."
[If you refuse to step into the portal] "Well, it looks like we won't be working together, no regrets Mr. Freeman"
[There's also another version of the one above] "Well, it looks like we won't be working together, no regrets Mr. Freeman, but there are a few survivors of your personal holocaust who would like the chance to meet the man responsible for the TOTAL ANNIHILATION of their race..." [Then you get teleported, with no weapons, in front of a lot of Alien Grunts and Controllers and the game ends with you dying]

Gman in Half-Life: Opposing Force:

"So... Corporal Shepherd, we meet at lasst. Please don't think that I've been avoiding you, a great many matters require my attention in these troubled times, I do hope you understand. And now I require a further indulgence on your part, I cannot close my report until every loose-end has been tied up.. the biggest embarrassment has been Black Mesa Facility but I think that's finally taken care of itself.."
[Nuke goes off]
"Quite so..."
"But there is still the lingering matter of witnesssses. I admit I have a fascination for those who adapt and survive against all odds, they rather remind me of myself. If for no other reason I have argued to preserve you for a time."
"While I believe a civil servant, like yourself, understands the importance of... 'discretion,' my emplopyers are not quite so trusting, and, rather than continually subject you to the irresistable human temptation of 'telling all,' we have decided to... 'convey' you somewhere you can do no possible harm... and where no harm can come to you. I'm sure you can imagine there are worse.. alternatives."
[Gman then walks through a portal leaving Corporal Shepherd in god-only-knows where, on his own]