HL2 begins with the assumption that you chose to work for the G-Man at the end of HL. What happened between HL and HL2 is uncertain, but throughout the game various clues exist so you can piece it together. For an in-depth view of what happened, go to this article (http://www.hlfallout.net/articles.php/article_23/) (the information therein was speculated upon prior to HL2's release, but has been verified, so it is accurate). While these events were taking place, Gordon was in some sort of cryo-sleep. He is awakened by the G-Man when the Combine are in total control of Earth. After a short speech from the G-Man, Gordon is put on a train heading into City 17, the base of operations for the Combine and also the office of Dr. Breen, Earth's administrator and intermediary for the Combine.

When he arrives at the station, it quickly becomes apparent that the citizens are being oppressed by the patrolling guards. A Scanner hovers towards Gordon and takes his picture. He makes his way through the station, but is halted at a checkpoint heading towards Nova Prospekt. A Combine Metrocop commands Gordon to follow him and leads him into an interrogation chamber that looks none too inviting. The Metrocop turns off the cameras ... and takes off his mask. It turns out to be Barney from Black Mesa.

Barney has infiltrated the Combine ranks and acts as a spy for the resistance. He flagged Gordon when he disembarked from the train so he could be taken separately (and, as will appear later, it would've been detrimental had Gordon been allowed to go on to Nova Prospekt). Dr. Kleiner tells Barney to send Gordon on to his lab. But before Barney can try anything, somebody starts banging on the door. Gordon is drummed out and told to make his way to Dr. Kleiner's lab. There's no other way than through a tenement block, and there, things start to go wrong. Gordon was flagged at the station but didn't go through the checkpoint, so there's a miscount in the area. The Combine are coming down hard in order to find the miscount. At this point, the train Gordon was supposed to board arrived at Nova Prospekt, so the Combine can compare the passengers with pictures taken at the station. That's how they find out it's Gordon who's missing. So he's recognized at the tenements and is forced to run from Metrocops ganging up on him from all directions. Gordon takes to the roofs but is cornered further on and knocked unconscious.

When he wakes up, he looks straight in the eyes of Alyx Vance, a member of the resistance. She took out the Metrocops and asks Gordon to follow her to the lab. There, Gordon is (re)introduced to Dr. Kleiner, Gordon's former professor at MIT and a survivor of the Black Mesa incident. He's apparently looking for Lamarr, his pet-something. But when he sees Gordon, his attention is immediately focused on the tasks at hand, which is to get Gordon suited up. Barney joins the party and is given the honour of revealing the new HEV suit to Gordon. But the ceremony is disturbed by Lamarr, which turns out to be Dr. Kleiner's pet Headcrab. Lamarr escapes into a ventilation shaft and is given no further attention. Gordon is then fitted into his trusty HEV suit and taught how to use the Combine chargers present throughout the city.

The idea is to get Gordon to Eli's lab which lies outside of City 17. Eli Vance is Alyx's father and another survivor of Black Mesa.

Dr. Kleiner's lab is outfitted with a teleportation device which can teleport anyone and anything directly to Eli's lab. Alyx goes first and joins her father successfully. But when it's Gordon's turn, Lamarr hops out of the shaft and jumps in the teleportation beam, thereby distorting the process and throwing Gordon into random locations. One of these locations is Dr. Breen's office, where Gordon appears twice. Dr. Breen is puzzled by the mysterious appearance of this man, who he seems to recognize as Gordon Freeman. When the harmonic reflux is over, Gordon ends up outside Dr. Kleiner's lab. There, he is told by Barney to make his own way to Eli's lab through the canals. Gordon's appearance in Dr. Breen's office has put the Combine on full alert. He is dubbed an 'anticitizen' as thousands of Scanners emerge from the Citadel.

The Railway and Black Mesa East
Gordon has no choice but to go through the canals. There, he meets up with resistance members who do their best to help him. They all seem to recognize Gordon and would gladly die for him. A rebellion movement known as the Railway exists throughout the canals. The Combine use many of their resources to hunt down Gordon, including flooding the sewers with manhacks and patrolling the surface with helicopters. As Gordon approaches the flood canals, another Combine tactic becomes clear. They bombard the area with shells that contain Headcrabs. They in turn infect any resistance members present in the area. Gordon is allowed the use of an airboat to make his way past the canals. It's a perilous journey, but he manages to plow through the Combine's defences. Thanks to a hunter rifle mounted on the airboat by a Vortigaunt, Gordon even manages to take out the helicopter that was hunting him. So, he survives the ride and reaches the dam, where Eli's lab known as Black Mesa East is located.

Gordon's arrival is met with enthusiasm, in particular from Dr. Mossman, a survivor from Black Mesa. She takes Gordon down to Eli's lab, where he is greeted by Dr. Vance himself. When Alyx arrives, she and Dr. Mossman get into an argument about some data. Eli butts in and asks Alyx to show Gordon the Zero Point Energy Field Manipulator, or Gravity Gun. Gordon and Alyx have some fun with it in the scrapyard at the back of the lab and meet up with Dog, Alyx's sidekick. Then the Combine Scanners show up, foreboding an attack. Alyx frantically tries to make her way back to her father, but is cut off from Gordon by a cave-in. Alyx commands Dog to open the passage to Ravenholm so Gordon can escape. So it's off to Ravenholm.

Ravenholm and the Coastline

Ravenholm is an old mining town inhabited by escapees from City 17. It was extensively shelled by the Combine, so all the inhabitants are now either dead or mutated. It will soon become apparent why the resistance members shy away from this place. Yet, there is still one human alive in Ravenholm who has taken it upon himself to "tend to his flock". This man is Father Grigori. Basically, he has set traps all over the place and skulks about, shooting at everything with his shotgun. Gordon is helped a great deal by Father Grigori, who shows him to the mines. The man himself wishes to stay behind. What happens to him is uncertain. Despite hordes of Zombies ganging up on him, he keeps fighting.

Gordon passes through the abandoned mines which are equally infested with all the Headcrab varieties. Afterwards, he makes his way to the surface and emerges next to a railroad. After dealing with a few Combine Snipers, he helps some resistance members take out a group of Combine Soldiers. They in turn put Gordon in contact with Alyx, who tells him that her father was captured in the attack on the lab and taken to Nova Prospekt. Gordon must meet up with Alyx there. But Nova Prospekt is still a long way off. So Gordon is given a buggy with which he can make his way across the coastline. It proves to be a dangerous trip, since not only do the Combine have checkpoints everywhere, but it's also mating season for the Ant Lions. So they're extra edgy and all over the place. Nevertheless, Gordon makes it to the outpost of Colonel Odessa Cubbage, a leader of the resistance. He gives him an RPGL and shows him how to use it. Right in time, too, because a Combine Gunship flies in and attacks the outpost. Gordon takes down the Gunship and can continue his journey.

When Gordon reaches Lighthouse Point, he is told that the Combine are looking for his buggy. Just then, Combine Dropships appear and the lighthouse is under attack. Gordon assists the resistance members in repelling the attack, and is then shown a secret passage along the cliffside. There, he sees that a Dropship flies off with his buggy. Nothing that can be done. Up ahead is another beach, but it's a breeding ground for the Ant Lions. A frightened civilian tells him that the Vortigaunt camp is up ahead, but getting there isn't easy. As soon as the sand is touched, mad Ant Lions pop up and attack the disturbance. Through clever use of his Gravity Gun, Gordon edges across the beach and reaches the entrance to the Vortigaunt camp. But first he has to deal with an Ant Lion Guard. When the thundering creature finally gives up, the door is opened and a Vortigaunt emerges. He retrieves the so-called Pheropods from the animal carcass. They fool the Ant Lions into thinking Gordon's their leader. Now he can use the previously hated enemies to his advantage. Because up ahead is a beachhead at the rear of Nova Prospekt. With the assistance of the Ant Lions who now do his bidding, Gordon breaches through the Combine's defences and infiltrates Nova Prospekt.

Betrayal in Nova Prospekt
Nova Prospekt is an abandoned prison facility turned into something much worse. The Combine tried their hardest to keep Gordon out of this facility (think back to the two Gunships at the entrance). The first part of the prison is a dilapidated series of hallways and cells. With the help of the Ant Lions, Gordon takes out the many Combine Soldiers that occupy the area.
Further on, he comes across an area which has been completely destroyed by a series of metal barriers. These are part of the Citadel. They slowly expand, crushing everything underneath and thus destroying all they touch. Past the barriers, Gordon finds another railroad...and Alyx.

Alyx found her way into Nova Prospekt aswell to look for her father. She's quite pleased to see Gordon and suggests that they get moving. With the help of a hacking device, Alyx manages to find Eli through a console. When she meets him, she sends him off to the Combine portal room. It's up to Gordon and Alyx to get there on foot. Alyx stays behind so she can help out Gordon through the security system. In a checkpoint up ahead, Gordon fends off dozens of Combine Soldiers while he waits for Alyx's arrival. When she does, she activates a console to see where Dr. Mossman is, who was also captured. She is shocked to see Judith talking with Dr. Breen. It seems Judith has been a spy for the Combine all along. This infuriates Alyx. She asks Gordon to move on, since time is now of the essence.

After an epic battle in the D8 prison block, Alyx joins Gordon again. Through the use of a console, Alyx locks Dr. Mossman in her office. She then confronts her. Judith tries to defend herself by saying she's working to the same end, but Alyx cuts her off and orders her to activate the Combine portal in the next room. There, Eli is wheeled in and everybody's ready to be teleported to Dr. Kleiner's lab. But when Alyx runs to a panel that has begun to sound an alarm, Dr. Mossman gets into the portal with Eli and teleports to an unknown destination. Desperate, Alyx feeds in the coordinates for Dr. Kleiner's lab. While the portal powers up again, more Combine Soldiers rush in. Gordon and Alyx fight them off while the portal charges. Afterwards, they successfully manage to teleport out of Nova Prospekt.

Street War

When Gordon and Alyx arrive in Dr. Kleiner's lab, there's nobody there. The door is carefully opened by Dr. Kleiner, and his loaded shotgun indicates he didn't know what to expect. Dr. Kleiner says he had lost all hope, because a week has passed since Gordon and Alyx teleported out of Nova Prospekt. There's an apparent time-lapse difference of one week between the Combine portal and Dr. Kleiner's teleportation device (which still uses Xen as a relay). And alot has happened in that week. The blow Gordon struck at Nova Prospekt was seen as a signal for the rebellion to start the uprising. Combine forces are overtly encountering resistance and are desperately trying to quell the anticitizens. Gordon himself has been named the Anticitizen One. Dr. Kleiner contacts Barney who's leading a push towards the Citadel. Barney asks Gordon to join him in the city so he can help out wherever possible.
Dog also made it out of Eli's lab in one piece and he seems extra pleased to see that his master is equally unscathed. Alyx orders Dog to help out Gordon. Alyx herself wishes to stay in the lab so she can get Dr. Kleiner to safety (who seems adament on finding that little pest, Lamarr). Dog and Gordon take to the streets.

Dog single-handedly deals with a bunch of Combine Soldiers and an APC, but then flies off while trying to bring down a Dropship. Gordon doesn't have to go it alone, however, as many resistance members roam the streets, all of them more than willing to join Gordon's side. City 17 is under complete martial law, and the Striders have been released. Gordon pushes through various checkpoints and makes it to an appartment block where he meets up with Alyx. Apparently, there are a few generators in the city, and they'll have to be disabled in order to weaken the Overwatch. After a hectic street battle, the first generator is disabled. Alyx and Gordon move past a gate towards a bridge that'll lead them to Barney. Unfortunately, the bridge has collapsed. While Alyx is scouting for another way across, she is engaged by Combine forces and has to move away. Gordon, unsure of her fate, has no choice but to move down the path Alyx pointed out to him. After a short stretch through the sewers, Gordon reaches the surface again, where he's told that Barney is pinned down by snipers on the roof of a warehouse. Gordon deals with the snipers and meets up with Barney, who leads him to the next objective.

Apparently, an old building in the centre square of City 17 ("a bank or a museum", as Barney puts it) has been converted to a Nexus by the Combine. Now it acts as a suppression field. This field will have to be shut down before a push towards the Citadel can take place. Barney's covert status as a Metrocop grants him access to certain areas, which comes into play once he and Gordon make it into the building. There, they manage to disable the three generators present, thereby shutting down the suppression field and allowing the rebellion to move through. Barney stays behind to let other resistance members through and Gordon heads for the roof. There, he has a clear view of the square, which has been turned over to the Striders. Gordon quickly heads downstairs to assist in the losing battle. After a heavy struggle, the Striders roaming the square are taken down.

Gordon moves past the Combine defences and heads towards the Citadel. The resistance has appointed a statue of a horse as a rally point. But the area is patrolled by many more Striders, and to top it off, a Gunship decides to drop by. Nevertheless, Gordon's determination and the aid of the many resistance members present aid in taking down the Combine forces. After an epic battle, Gordon makes it to the horse, where Barney and Dog show up. Dog is apparently focused on the Citadel, he seems to think Alyx is somewhere in there. Despite Barney's negativity, Dog succeeds in lifting a Citadel barrier in order to reveal an opening for Gordon to move through. Here, Gordon's part in the street war ends as he makes his way into the bowels of the Combine headquarters.

The Citadel, Dr. Breen Speaking
At the base of the towering monolith resides a massive tunneling device designed to strip the earth beneath it of minerals and resources. Gordon makes his way past steep cliffsides to reach the base of the Citadel. He sees no other way into the heart of the structure than taking a ride in a mover, which runs throughout the Citadel. He is immediately flagged and dropped off at a checkpoint, where a desintegration field confiscates all his weapons. But when the field attempts to destroy the Gravity Gun, the unexpected gravitational pulse destroys the field and somehow super-charches the Gravity Gun. Gordon picks it back up and uses it to plow through the oncoming Combine forces. With the new Gravity Gun (which instantly kills any troopers caught in its field), Gordon tears through the forces the Citadel spews out. Dr. Breen occasionally adresses him through video screens, commenting on his (lack of) accomplishments.

Higher up in the structure, Gordon has no choice but to take another ride in a mover. This one brings him all the way to the top of the Citadel, into Dr. Breen's office, where his Gravity Gun is confiscated (manually, this time). Dr. Mossman welcomes Gordon and tells him to keep calm. She leads him into Dr. Breen's office, who is talking to Eli about the vastness of the universe. When Gordon enters, all attention is focused on him. A Combine Elite leaves the Gravity Gun on the desk. Dr. Breen states that he now holds all the cards concerning Earth and the Combine. His only problem is the rebellion. He wants Eli to convince the resistance to give up its senseless struggle. Eli won't have any of this and refuses to cooperate. Then Gordon finds out what happened to Alyx. She was captured and brought up to the office. Dr. Breen uses her as leverage, and when they both refuse, he threatens to send them both through a Combine portal. He then adresses Freeman, attempting to convince him into joining his cause. Gordon could serve well as a new resistance leader.

But then the tables turn. Dr. Mossman pulls out Alyx's hacking device and disables the teleport controls. Dr. Breen calls for help, but the intercom is destroyed aswell. While Judith attempts to free Gordon, Dr. Breen panics and picks up the Gravity Gun. He attempts to use it on the others present, but because he holds it upside-down, it knocks him back and at the same time, frees Gordon, Eli and Alyx. Dr. Mossman hands Alyx her hacking device, who asks her to take care of Eli. Then she and Gordon go after Dr. Breen.

Dr. Breen's plan has failed, and he wishes to escape as soon as possible. He's online with the Combine Advisor, claiming he can still deliver Earth, when he is disturbed by Gordon and Alyx. Dr. Breen runs for an elevator and manages to flee. Alyx tries to find out where he's going and unveils a Dark Fusion reactor at the tip of the Citadel. Dr. Breen is trying to teleport out, and Alyx asks Gordon to stop him. Fortunately, Dr. Breen left the Gravity Gun near the controls, so Gordon can measure up to the Combine forces ganging up on him as he tries to make his way to the reactor.

Dr. Breen is inside some sort of teleportation field, which, at the moment of synapse, will collapse and destroy everything around it. Gordon makes it to the tip of the reactor, where a huge portal starts to open. Two Gunships emerge from the portal, but with handy use of the Gravity Gun and the nearby flow of energy clusters, Gordon manages to take them down. He then proceeds to hurl more energy clusters into the reactor, thereby destabilizing the process and shutting it down. Dr. Breen is now trapped inside the teleportation field. But the reactor is still destabilizing. Alyx urges Gordon to try to make it out of there, but then the reactor explodes.

And right then, time seems to literally stop. Everything is frozen, including the explosion. And then, an all too familiar voice is heard. It's the G-Man. He appears out of nowhere and congratulates Gordon on his accomplishments. Gordon is teleported away from the Citadel. The G-Man comments on various employment offers and states that he will choose for Gordon. He then leaves Gordon, who is once again trapped.

THE END

Read on for explanations and speculation.

What does it all mean?
HL2 once again manages to tell a story without the use of cut-scenes. But the fact remains that the story is quite a vague one. What follows is my view on the underlying plot and the way everything is put together (Note: this is my view and it may differ from yours. Please don't tell me I'm wrong, because I most likely am).

After the Combine take over Earth, Dr. Breen launches his propaganda that the Universal Union (as he calls it, "Combine" is actually an unofficial expletive) is mankind's next step in evolution. Not everybody agrees (in fact, very few people are happy about it), and an underground rebellion is formed. Dr. Breen wishes to deliver Earth to the Combine, but this resistance is standing in his way. To top it off, one of their leaders is his former collegue, Dr. Eli Vance. There are various clues throughout the game that tell you why Gordon was brought into City 17:

1) A public transmission from Dr. Breen states that Dr. Eli Vance could've been captured at any moment, but his capture only took place when Freeman arrived at Eli's lab. This way, Dr. Breen could illustrate what the consequences would be of harbouring an anticitizen.

2) When Gordon has his face-to-face with Dr. Breen, he is told that his contract was open to the highest bidder.

Dr. Breen had his own plan to quell the rebellion. He buys Gordon's contract from the G-Man and lets him loose in City 17. Gordon has obtained a near messianic status in his absence since Black Mesa, so he is welcomed to the resistance. This resistance is heavily influenced by Black Mesa, using the Lambda logo to denote supply caches, for instance. This plan seems to backfire somewhat, because Dr. Breen must answer to the Combine because of his actions and the lack of success in Gordon's capture.

Dr. Breen assumed Gordon would fail. And when he is captured inside the Citadel, everything comes to plan. Dr. Breen wishes to enlist Gordon as a new resistance leader, but one under Combine control, so the rebellion can be told by the one free man himself that it's useless to resist. Should Gordon refuse to cooperate (most likely, but since he's never given the opportunity to talk, we'll never know), Dr. Breen can use him as living proof that even a messiah figure like Gordon can't stop the Combine.

In the end, it's one traitor who destroys everything Dr. Breen has built up. Dr. Mossman betrays him by freeing Gordon. The resulting panic forces Dr. Breen to escape Earth. But Gordon manages to stop him. The resulting cataclysmic explosion seems large enough to wipe out the entire Citadel, let alone the whole city beneath it. But exactly what happens, we don't know for sure, since the G-Man extracts Gordon just seconds prior to the blast.

So now the G-Man is once again in control. Gordon must again wait in cryo-sleep for his next assignment, whatever that might be. Let us hope a future sequel will shed more light on the mysterious storyline that is heir to HL2.

P.S. There's a very thorough guide on the entire HL and HL2 universe located here (http://fragfiles.org/~hlstory//). I suggest you pay it a visit, since it's a very useful piece of work. The author's views only differ from mine on one subject: whether Gordon is doing contract work in HL2 or not. But, like I said, this page is speculation. And that's where all the fun lies.