To start things off…
WARNING! SPOLIER ALERT
I personally think the story goes like this…
The Half-Life series begins in 200-, at the Black Mesa Research Facility, deep below the New Mexico desert.Gordon Freeman, a recently employed theoretical physicist for Black Mesa, is involved in an experiment analyzing a strange, unknown crystal. On his way to the testing chamber, he sees a mysterious and enigmatic government man watching him from a tram, and again arguing fervently with a scientist. After slipping into his trademark HEV Suit, he makes his way to the laboratory, meeting several nervous colleagues on his way. Inside the large, cylindrical chamber, the scientists assure Gordon that nothing will go wrong, and he makes his way, confidently, to flip the switch. Below him, Gina Cross delivers the non-standard crystal to the delivery shaft.
Powering up, the tunneling rods of electric current jump from the top of the Anti-Mass Spectrometer to its base, signaling that the machine is ready to begin. The specimen for analysis is lifted into the chamber in its cart. Gordon begins the experiment by pushing the crystal into the beam. Suddenly and furiously, the crystal causes severe discrepancies in the equipment, causing explosions and destruction in the surrounding area. Trying their best to shut it down, the scientists in the observation area shout manically. Gordon is somehow teleported out of the facility onto a strange alien world, where he is confronted by aliens and monsters alike. Saved from the destruction, for now, he has no idea of the trouble the crystal has caused.
When he arrives back into the chamber, a scene of destruction and terror surrounds him. The Anti-Mass Spectrometer, now hanging loosely on its hinges and exploding every five seconds, has thoroughly fallen apart and is on the floor in pieces. One of three surviving scientists, Eli Vance, helps Gordon on his way, but not before Gordon has a chance to see an odd alien teleporting in out of nowhere. It seems that, throughout the rest of the facility, aliens are appearing, and attacking scientists without mercy. The few who have survived are fleeing to the surface.
Traveling further through the facility, Gordon learns that the HECU forces have been called in to control the situation, however quickly discovers that their idea of containment is to kill everyone and everything within Black Mesa. A security guard informs him that he is to reach the Lambda Complex at all costs, and on his way launch a satellite which can be used to close the rift. He continues his journey using a disused rail system below the Facility. At the end of the line, he launches the satellite needed by the Lambda team to close off the rift. Continuing along on the surface, Gordon comes across the Black Ops assassins, who were brought in after the HECU repeatedly failed to dispose of Freeman, however they also fail to stop him. He is apprehended by the HECU, and they stash him in a trash compactor. This also fails, and Gordon wakes up in time to get out and find his way back in.
When Gordon reaches the Lambda Complex, he is teleported to Xen in order to kill the creature responsible for keeping the rift from closing. Before he leaves, a scientist gives him the Long Jump Module, which can be used on Xen to make the necessary jumps. Xen, an impossible world of floating islands, is even more full of hazardous aliens than Black Mesa has become, and Gordon swiftly makes his way to the Nihilanth’s lair. On the way, he is caught up in a battle with the Gonarch, which he wins.
The Nihilanth greets Gordon with threats, and uses powerful yellow projectiles to take down Gordon. Luckily, Gordon manages to destroy it and the rift begins to close. As the Nihilanth’s fading last words echo in Freeman’s mind, the G-Man absconds Gordon and stores him in stasis, after telling him that he has been offered employment. Walking into the green portal, Gordon accepts his offer and disappears from the face of the planet.
Nearly twenty years later, the G-Man brings Freeman out of stasis and places him onto an Earth ruled by the Combine, an alien race that used the dimensional rift caused at Black Mesa to conquer Earth. In City 17, Freeman meets surviving members of the Black Mesa incident, including Isaac Kleiner, Barney Calhoun, Eli Vance and his daughter Alyx Vance, and aids in the human resistance against the Combine. The Xen aliens, the Vortigaunts, who have also been enslaved, assist the Resistance. When Freeman’s presence is made known to former Black Mesa administrator and Combine spokesman Wallace Breen, Freeman becomes a target for the Combine. Eventually, Freeman sparks a full revolution amongst the human citizens, by destroying the Nova Prospekt prison facility, where the Combine used to manufacture humanoid soldiers. Eli Vance and his daughter are subsequently captured by the Combine, and Freeman helps the resistance forces attack the Citadel to rescue them. Breen attempts to flee in a teleporter, but is killed when Freeman destroys the dark energy reactor at the top of the Citadel. The G-Man then arrives to extract Freeman before he is killed in the explosion, but is interrupted when Vortigaunts liberate Freeman from stasis and place both him and Alyx Vance at the bottom of the Citadel. After Dog finds Gordon in the rubble, Alyx and Gordon attempt to stabilize the Citadel’s primary reactor while the citizens evacuate the city. Alyx and Gordon soon discover that the Combine is attempting to destroy the reactor to call for reinforcements from the Combine’s native dimension. After downloading critical data, they move through the war-torn city to the train station to take the last train out of the city. The Combine then destroys the reactor, thus destroying both the Citadel and City 17; the resulting explosion of which causes the train to derail.
Freeman awakens in one of the wrecked train cars with Alyx outside, where a superportal is visible from where the Citadel used to stand. They begin a journey through The Outlands to White Forest, a Resistance-controlled missile base in the nearby mountains. Along the way, Freeman and Alyx are ambushed and Alyx is severely injured by a Hunter. However, a group of Vortigaunts are able to heal her. After Alyx is healed, both her and Gordon are able to reach the Resistance base and deliver the data, which contains the codes to destroy the superportal as well as information on the Borealis, an enigmatic research vessel operated by Black Mesa’s rival, Aperture Science. The base then launches a rocket that is able to shut down the superportal, cutting off the Combine from outside assistance. However, as Alyx and Freeman prepare to travel to investigate the Borealis, they are attacked by Combine Advisors, who kill Eli Vance before being driven off by Dog.
Credits to Combine Overwiki for story.
