Storyline
«Canon itself is non-canon» — Mark Laidlaw©
Info were taken from Half-Life 2 Wiki
Intro
Gordon awoke beside the G-Man who shows him bits of what happened during the last 10 years, but without telling much. Gordon then finds himself on the Wasteland Train and encounters Samuel, a citizen who tells him some bits of information about his life and gives him some hints about what is going on. The train ride allows the player to view the Wasteland outside City 17, with ruins, wrecks, Houndeyes, Bullsquids, and other unknown fauna. Another nearby train is seen being attacked by a Gargantua, but the monster is destroyed by the heavy engine. The Wasteland Train then proceeds inside the city, first through Outer City, ruined, and then Inner City, the Combine-converted city, surrounded by a huge concrete wall protecting it from the Wasteland hazards. Creatures can be seen killing themselves on the barricades. Gordon glimpses Citizens in their apartments. The train arrives at last at the station, and Cremators can be seen cleaning around the train from Bullsquids or Headcrabs that managed to get inside the perimeter.
City 17 Trainstation
After his arrival at the trainstation, it is unknown what Gordon does, sees and who he meets. It is probable that he meets Barney who shows him the way and tells him to meet him near the Manhack Arcade.
Industrial Site
Gordon didn't leave the trainstation through the main entrance, but through a back door that leads to an industrial part of the city, with noisy factories filled with citizens working and passing through in all directions, watched by Metrocops and Combots. Workers consist of adults but also children. Gordon discovers the Cremator Factory, where children are building Cremators, and other workshops. He also discovers the Vorti-Cells, used as stations siphoning power from trapped Vortigaunts (although it is likely that they could be found everywhere in the city). Gordon then eventually reaches the Trainstation Plaza and proceeds on foot to the entertainment / commercial part of the city where Barney is waiting.
Terminal Plaza
Gordon walks through the Trainstation Plaza and gets to see the trainstation main facade and how Citizens are treated by Civil Protection. He then proceeds to the Manhack Arcade through yet to be identified areas, probably apartment buildings, though it is unknown, and, at some point, an area under construction. It is also unknown when Gordon was to be chased by Civil Protection through apartment buildings, since it seems he was to be rather left alone in most of the maps relating the game's beginning.
Manhack Arcade
In an entertainment / commercial area where City 17's civilian life was to be shown, Gordon sees his first Breencast (or rather "Consulcast" at this point), a Metropolice station and discovers the Manhack Arcade, an entertainment place where Citizens play video games consisting in controlling Manhacks into the streets and killing fugitive Citizens, ignorant of the fact that the Manhacks they are controlling are real and are actually killing Citizens on the streets. Gordon then meets with Barney, who works undercover as a Metrocop, and proceeds to Kleiner's Lab through the sewers. It is unknown if Gordon meets Barney there for the first time or in the trainstation like in retail.
Kleiner's Lab
Gordon reaches Kleiner's Lab where Kleiner is astonished to see him. He also gives him the physics manipulator. Then Gordon introduced to the teleport. He is to be sent to Kraken Base (where Helena Mossman is waiting), since Eli's lab teleport is in pieces and therefore not working. Like in the retail version of the game, the teleportation fails and Gordon must instead flee on foot to Eli's lab in the scrapyard. He leaves City 17 through the Canals.
Sewers / Canals
Gordon leaves City 17 on foot, then with a Jet Ski, according to the original concepts. He encounters Barnacles, Headcrabs, Houndeyes and Bullsquids on his way while he is getting outside to the Outer City. It was supposed to be much bigger and longer.
Zombie Town
At the end of the canals Gordon arrives at a small lake and discovers the yet unnamed industrial town filled with zombies and traps set by a mad monk. At some point he would use a vehicle called the "digger" to proceed through mines and destroy a Combine Big Momma Pod laying Headcrabs to clear the way.
Antlion Caves
After leaving Eli's Lab, Gordon goes through caves filled with Antlions and Antlion Grubs, and confronts an Antlion Guard. It is unlikely that the player was already to be able to tame Antlions at that point of the game's development. It is unknown if Alyx is there for the remainder of the journey.
Eli’s Lab
Gordon reaches at last the scrapyard. There he encounters Eli Maxwell, Dog and possibly Alyx in the very simple and rough Eli's lab, inside a cave. Eli shows Gordon a slideshow of what happened during the last 10 years, including the loss of his leg.
Wasteland Depot
Gordon's train arrives at a Combine train depot, simply called the Depot. He proceeds through the wasteland into the lighthouse. The train depot is built near an unnamed old prison where Gordon fights Combine soldiers, possibly with the aid of Antlions, although they can harm him as well. He then discovers the Gunship Bays, where Gunships are built. Antlions attack, fuel tanks explode and the whole place is engulfed in flames. Then Gordon goes into the Depot itself through the cargo conveyor and takes another train to the Air Exchange.
Air Exchange
Gordon's train crashes in another depot before the Air Exchange, a Combine facility replacing the air by noxious, murky gases with its main reactor. He is met by Alyx. There they are attacked by Combune Guards and Striders. He meets Alyx's father, Captain Vance, and his Conscripts, and a battle is likely fought. During or after the battle, Gordon proceeds on foot to the AirEx. He then must reach the top of the highest tower, battle a Gunship and then jump into a pool of industrial solvents at its base. He then must go inside the main reactor of the facility, protected and operated by Stalkers, and sabotage its core, making the Air Exchange completely nonoperational and seen as a signal to start the human uprising in City 17. Gordon then reaches the shore on foot. Alyx likely leaves at some point after the battle, since it is likely that Gordon is alone.
Arctic regions
Arriving at the shore, Gordon proceeds to the Arctic regions on a tugboat.
Borealis
Arriving on the site of the Borealis with their tugboat, the ship either being stranded in the ice or drifting in the sea, Gordon and Odell visit the ship filled with the corpses of the Borealis Workers, Stalkers, zombies, tanks containing Combine Assassins (probably in stasis) and Combine soldiers. Gordon meets with Odell, former engineer of the Borealis. They leave the ship with a small submarine and proceed to the nearby Kraken Base, headed by Dr. Helena Mossman.
Kraken Base
Gordon and Odell reach Kraken Base in their submarine and encounter Helena Mossman, Kraken's director. Kraken Base is a rebel scientific base located beneath the sea. It is unknown what happens there and what happens to Odell and Mossman. Some battle with Stalkers was to take place while Mossman would reveal her double agent role, and the base would be heavily damaged. Gordon leaves, on foot, and reaches the Combine Weather Control.
Weather Control
Was to be set in and around a large domed facility influencing Earth's weather, located in the Arctic regions. There a massive attack would be led by Captain Vance and his Conscripts, aided with Alyx and Gordon. Its appearance is relatively unknown since Valve never published official images of it, nor can it be found in the Beta files. Gordon fights there alongside Captain Vance, his Conscripts and Alyx. They are attacked by "Synth". After that, Gordon and Alyx goes back to City 17 with a helicopter.
Palace
Heli crashes into housing of a museum. Alyx is injured and kidnapped by the Combine. Gordon must find her father Captain Vance. While making his way through the palace he comes across Female Assassins in certain areas and kills them. He joins the Conscripts through the rooftops in the ensuing uprising.
Street Wars
Gordon starts the street wars with the Conscripts on the rooftops at the foot of the Palace then finally reaches ground level, where a Overwatch Sniper has pinned down Conscript forces, including Peters who is stuck in a APC that got hit by a landmine. Manwich tries to save Peters but gets too cocky and runs at the sniper saying "You want me? You want some of me? Get it Get!" and he says that the sniper shoots and kill Manwich as another Conscript says that Manwich is down. After saving Peters by going to the APC and taking a RPG to kill the sniper the level ends with him thanking Gordon. At some point, Gordon manages to join Vance's Headquarters and Alyx, then proceeds behind the inner gates of the Citadel's outer wall. While there the Conscripts were to have a friendly Crab Synth. Further instructions would likely have been given there. He also journeys again in the City 17 underground, where he confronts many Hydras. Among others, Rebel forces fight Striders with tanks and RPGs.
Citadel
Gordon proceeds through the Citadel to finally reach the Consul office. There he confronts the Consul and finds Alyx being kept prisoner and discovers that Helena Mossman betrayed them. The original fate of Alyx Vance, Eli Maxwell, Captain Vance and Helena Mossman are unknown.
