It looks like the Combine Overwiki has a superior, more thoroughly researched Half-Life timeline. My timeline is missing details from Half-Life: Decay, Half-Life 2: Episode Two, the Portal 2 ARG and Portal 2 itself, although it does have some idle conjecture that you might find interesting.
The Combine, an exceptionally advanced other-dimensional race of whom very little is currently known, attack the "border world" of Xen. The dominant intelligent lifeforms on Xen are the vortigaunts. The Nihilanth, who may or may not already be the leader/ruler/tyrant/queen/mother of the vortigaunt race, is enslaved by the Combine and placed (possibly willingly) as a puppet ruler, leading the planet in the Combine's name. The vortigaunts are in turn enslaved with the metal collars which they are seen wearing in the original Half-Life games.
Aperture Science is founded by Cave Johnson, for the purpose of producing shower curtains.
The Eisenhower administration awards Aperture Science a contract to produce shower curtains for all US military branches except the Navy.
Gordon Freeman is born.
Cave Johnson is exposed to mercury and becomes insane.
Adrian Shephard is born.
Terminally ill and believing that time is flowing backwards, Cave Johnson initiates research into (among other things) quantum portals through space.
The Aperture Science Self-Esteem Fund For Girls is founded.
Surprisingly, actual progress towards the portal technology is revealed during a Senate investigation of Aperture Science. The company is awarded an open-ended contract to continue the research.
|1981 to 1985
Work continues on the "Portal" project.
GLaDOS v1.07a and v1.09 released.
Cave Johnson has a user account created for him, or else his existing account details are transferred over from whatever internal computer system was in use at Aperture before this time.
Black Mesa Research Facility begins working on similar teleportation technology to the Aperture portals. In response, work on GLaDOS, the Genetic Lifeform and Disk Operating System, commences at Aperture.
This is after GLaDOS v1.07 has been released, but time was flowing backwards, so who knows?
The Aperture Science research vessel Borealis disappears from its dry dock, taking part of its dry dock with it.
Black Mesa scientists experience some success in their teleportation experiments and discover how to travel between Earth and the border world of Xen. They are unable to travel freely from place to place on Earth, because Xen is in the way. However, orange crystals are discovered on Xen, which, when connected up to a relay device which is placed permanently on Xen, can be used to bounce the signal from Xen back to Earth accurately. Contact is lost with the survey team which set up the relay, though the relay itself possibly remains functional for a little while longer.
Black Mesa scientists soon discover a new way of aiming the teleportation field, using Xen as a dimensional slingshot, allowing teleportation between points on Earth without any need for equipment to be stationed on Xen.
A much larger teleporter, the Lambda Complex machine, is constructed.
Many samples of Xen fauna, including snarks, head crabs, barnacles, houndeyes and a Tentacle are brought from Xen back to the Black Mesa Facility for study. Xen-like environments are created to contain them. A domesticated barnacle is produced. Study of the mysterious orange crystal found on Xen also continues. Isaac Kleiner's pet headcrab, Lamarr, is possibly captured and debeaked at this point.
After ten years, GLaDOS is now an adequately functional Disk Operating System. Work begins on the Genetic Lifeform component.
|Several years later (1999?)
The Aperture Science Handheld Portal Device is completed.
By this time GLaDOS has been developed into her familiar "hanging computer" configuration. Doug and Henry are two Aperture employees working on her artificial consciousness, and have attached three different AI cores (Cake, Curiosity and Anger) to GLaDOS in an attempt to prevent her from trying to kill everybody in the facility. A fourth core, Morality, is developed and attached to her.
The first annual Bring Your Daughter To Work day takes place at Aperture. Chell, the adopted daughter of an Aperture employee, is in attendance, and agrees to be tested in the Computer-Aided Enrichment Center. She is placed in a Relaxation Vault. Meanwhile, GLaDOS is fully activated for the first time as part of several planned activities for the day.
The activation of GLaDOS is noted in the NOTES file on the Aperture Science intranet.
This is the last update made before GLaDOS malfunctions and floods the facility with a deadly neurotoxin. The scientists successfully install a Morality Core to shut the neurotoxin emitters down, but the facility is nevertheless fully evacuated. Chell is left behind inside her Relaxation Vault.
|May 5, 2000?
Gordon Freeman is sent a letter offering a job at the Anomalous Materials Laboratory of the Black Mesa Research Facility at Black Mesa, New Mexico, United States. Between now and May 15 he returns from his present post as visiting fellow at the University of Innsbruck and is trained in the use of his HEV suit.
|November 1, 2000?
Adrian Shephard is given his soldier's manual.
Scientists from Black Mesa successfully steal one of the four gigantic orange crystals in the Nihilanth's lair on Xen. This is the largest and purest sample retrieved so far and is the sample used in the anti-mass spectrometry experiment at the beginning of Half-Life.
The G-Man decides to cause a resonance cascade at Black Mesa Research Facility.
|March 3, 2001?
Shephard is in boot camp still. He hears rumours of the G-Man observing proceedings.
Shephard sees the G-Man for the first time and believes he is observing him personally.
Shephard and his unit, the Hazardous Environment Combat Unit, commence one week of solid training in indoor strategic combat but are not told why.
Shephard hears the Black Mesa facility being mentioned a lot and becomes convinced he is being primed for a mission.
Shephard has the rumour confirmed and is told to prepare for the event to happen tomorrow.
|~8:30am, March 16, 2001?
A major system crash at the Black Mesa Research Facility, orchestrated and triggered by the G-Man (before he officially arrives for the day), prevents scientists Dr. Isaac Kleiner and Eli Vance, who will be overseeing the morning's anti-mass spectrometry experiment, from knowing the dangerous properties of the sample which they will be analysing.
Doctors Gina Cross and Collette Green arrive for their morning's work and collect their HEV suits from the tubes flanking Gordon's. Because of the system crash they have to be re-added to the security database.
Barney Calhoun arrives by monorail to take over security duties at the beginning of his shift. The door to his workplace jams as a result of the crash, just as Gordon Freeman passes him in another monorail car, also arriving for his morning's work.
Both Barney and Gordon observe the G-Man while he is inbound by monorail.
On a security screen, Barney observes the Xen sample arrive at the Anomalous Materials lab, pushed by Gina Cross.
The G-Man arrives at Anomalous Materials lab, ahead of Gordon.
Gordon Freeman arrives at the Anomalous Materials lab and collects the third and final HEV suit.
Messing about in the lab kitchen, Gordon nukes the microwave casserole of Dr. Arne Magnusson. Magnusson develops a grudge about this.
Gordon observes but does not overhear Eli's brief conversation with the G-Man, in which the G-Man presents the new Xen fragment to Eli and advises him to "Prepare for unforeseen consequences" during the forthcoming experiment.
Collette Green activates the anti-mass spectrometer. Gordon pushes the Xen sample into the beam, causing a resonance cascade. The Anomalous Materials laboratory and much of the surrounding Facility sustains massive damage as large random quantities of matter are spontaneously transported to and from the world of Xen, including dangerous Xen fauna which is teleported into the Facility. Chaos erupts.
Eli Vance instructs Gordon to attempt to reach the surface and get help. Barney Calhoun, who is in a recently-repaired elevator at the time of the cascade, independently sets out to escape the facility too.
Since Gordon never returns, Eli eventually escapes the facility by himself.
Alyx Vance is extracted from the Black Mesa Research Facility by the G-Man.
Alyx is given an initial "appraisal" by the G-Man's "employers" but they fail to see any value in her.
The G-Man reluctantly releases Alyx back to her father, but continues to take a constructive interest in her development.
Gordon spends an entire day fighting his way through the damaged Facility towards the surface. By the time he gets there he has encountered the G-Man's special forces coming the other way, with instructions to kill all the civilians they find as part of a government cover-up. Gordon kills a large number of the grunts.
Barney's experiences are much the same, until Barney meets Dr. Rosenberg, who proposes an escape plan involving the original prototype teleporter (mentioned above, around 1986).
|Night of March 16
Gordon continues to trek through the BMRF interior, kills a Tentacle and accesses an old subway system which leads towards the Lambda Complex at the far end of the Facility. Before dawn, Gordon successfully launches a rocket containing a satellite which the surviving scientists in the Lambda Complex need to shut down the link to Xen.
Meanwhile, Barney and Rosenberg reach the prototype teleporter. Being an old model, it is not capable of moving objects from place to place on Earth; it can only send you to Xen or bring you back. As a result, Barney has to be sent to Xen to reactivate the relay which Black Mesa scientists originally left there. The relay's purpose is to seamlessly transmit the travellers from Xen back to a point on the outskirts of Black Mesa. Barney is then sent to collect power cells for the teleporter as well.
|Morning of March 17
By the time day has broken, mysterious Black Operatives have joined the invading human forces.
By this time the effects of the resonance cascade have long ceased, but more and better-armed aliens are still teleporting in. This is because a formal invasion force has now been mounted from Xen, under the command of the Nihilanth. Earth is now in a de facto state of war with Xen.
Gordon is captured by disgruntled grunts. Barney Calhoun, Rosenberg, Walter and Simmon(d?)s successfully teleport out of the Black Mesa Facility. Barney is briefly teleported to several other locations, and witnesses Gordon being dragged away by the grunts before snapping back to the exit tunnel and leaving the Facility safely.
Gordon is put in a garbage compactor by the grunts.
Adrian Shephard and the rest of his Hazardous Environment Comabt Unit are among the last grunts to be airlifted in to Black Mesa. Shephard is shot down by a Xen hovership before he can can be given any orders. He sets out on his own expedition through the Black Mesa Facility.
Gordon Freeman escapes the garbage compactor into the Facility's Residue Processing system and spends the rest of the morning making his way to Lambda Complex.
With Xenian forces overwhelming them, the human forces are told to forget about apprehending Freeman and pull out. Adrian Shephard attempts to join the evacuation but is prevented from doing so by an unsympathetic G-Man - who, despite appearances, does not actually leave the Facility at this point. Several other HECU soldiers are also left behind. The black ops remain on the site, however, and Shephard runs into them several times. The black ops are now, in turn, tasked with exterminating the grunts.
|Afternoon of March 17
Gordon reaches Lambda Complex where he is told that the satellite he has launched cannot be used to close the Xen rift because the Nihilanth is holding it open. Gordon is sent to Xen to kill the Nihilanth. Xenians attack the Complex just as Gordon leaves, damaging it, destroying Gordon's route home. Adrian Shephard arrives at Lambda Core just in time to witness Gordon departing for Xen.
Gordon succeeds in killing the Nihilanth. The G-Man, having observed Freeman's progress with great interest, consults with his "employers", extracts Gordon from the Nihilanth's chamber and offers him a job, which Gordon accepts. Gordon is placed into slow teleport, "awaiting assignment", and time ceases to pass for him.
The vortigaunt race is freed by the death of their immediate master.
Meanwhile, Shephard escapes Lambda Complex into the Black Mesa animal laboratories. He defeats a Pit Worm and makes it to the surface again at around dusk.
Because they are killed, the scientists of Lambda Core never actually manage to use the satellite to close the Xen rift. Not only does the rift remain partially active (if not fully open), the satellite remains in orbit, unused.
Shephard encounters Black Operatives planting and arming a nuclear device, intending to destroy the entire Black Mesa facility as a last-ditch attempt to prevent what is happening. Shephard disables the weapon, but the G-Man, after inspecting Shephard's work, reactivates it.
Shephard continues onwards to where he encounters a Gene Worm coming through from Xen and defeats it.
The G-Man extracts Shephard from the Gene Worm arena, and, with the permission of his "employers", places him into a slow teleport for possible future reference. The nuclear bomb goes off, destroying the entire Black Mesa Research Facility.
While scientific masterminds Eli Vance, Isaac Kleiner and others successfully escape the detonation, all their notes and equipment are destroyed. Human teleportation science takes a step backwards.
|Over the next 20 years
Following the death of the Nihilanth, freed vortigaunts from Xen migrate to Earth for relative safety, and the Combine become aware of the planet Earth and the still-open rift between it and Xen.
Portal Storms occur - due to the rift or the Combine or both - dropping dangerous fauna from Xen on the Earth. The countryside becomes swarmed with antlions and headcrabs and the oceans fill up with killer leeches. Humans withdraw into fortified cities.
With the human race at its weakest point, the Combine open a "super-portal" and launch a full-scale invasion of Earth. The Seven Hours War occurs. Wallace Breen, former administrator of Black Mesa Research Facility, quickly negotiates humanity's surrender to the Combine. Breen, like the Nihilanth before him, is willingly placed as the "friendly face" of the Combine aggressors, genuinely believing that
This is Alyx Vance's childhood.
Cities are stripped of their names and numbered instead. Various fields are set up which:
Combine citadels are established in cities. The Combine begin draining the oceans and harvesting useful minerals from the Earth, sucking it dry. Nova Prospekt, a prison near City 17, is set up as a major Combine base (experimentation facility and teleporter landing pad connecting their universe to ours). Experiments on humans produce the Combine Overwatch soldiers - the human equivalent to vortigaunt slaves - and the fearful subhuman Stalkers. Soon it has become routine to transport humans to Nova Prospekt by train in order to convert them into Stalkers. Captured refugee vortigaunts are also sometimes taken to Nova Prospekt - being telepathic, they are sometimes able to send pictures back to the resistance before being tortured and killed.
Eli Vance, Judith Mossman, Isaac Kleiner, Barney Calhoun, Alyx Vance and Arne Magnusson are among the survivors of Black Mesa who make their way to City 17. Discovering what is happening at Nova Prospekt, they set up an "underground railroad" to ferry incoming human "livestock" out of City 17 to safety. Barney Calhoun infiltrates the Overwatch and works undercover to assist in this; Kleiner (along with his headcrab Lamarr) operates out of a lab near the inbound railway station; Mossman and the Vances work out of "Black Mesa East", a lab near the town of Ravenholm.
A large number of resistance members and several sympathetic vortigaunts end up working on this railroad, which is signposted with yellow Lambda symbols. However, it still involves a long trek down the old canals to get to Black Mesa East, so the scientists begin work on a teleporter which can make this journey infinitely easier.
The rescued proles, possibly including Father Grigori, colonise the abandoned nearby mining town of Ravenholm.
Ravenholm is bombed with headcrab-filled missiles. The headcrabs assimilate most of the town's population, with the notable exception of Father Grigori. The survivors, if there are any, escape through the mines to the coast.
The underground passage from Black Mesa East to Ravenholm is sealed off to prevent the headcrabs from spreading. "We don't go there anymore."
|Red Letter Day
Isaac Kleiner completes the new underground railroad teleporter.
Gordon Freeman is woken by the G-Man and reinserted into reality on a train inbound to City 17 and Nova Prospekt.
Barney Calhoun (in his disguise as a member of the Combine Overwatch) spots Gordon and helps him escape. Freeman is eventually rescued from Civil Protection by Alyx Vance and taken to Kleiner's lab. Alyx is successfully teleported to Black Mesa East but Gordon's jump fails and he is forced to use the "underground railroad".
Gordon momentarily appears in Wallace Breen's office during the failed jump. Breen instantly recognises him and alerts his Combine Advisor superior. Within hours the entirety of Civil Protection is after him.
Though the underground railroad and most of the people maintaining it are destroyed by this unprecedented movement, Freeman reaches Black Mesa East by nightfall.
Around this time, Judith Mossman makes a deal with Breen to turn Freeman over to the Combine in exchange for the safety of Eli Vance. She argues that Eli will eventually come around to the Combine point of view: the truth is that she has personal feelings for him.
|Night of RLD
Having covertly followed Freeman, the Combine jump the gun, launching an attach on Black Mesa East without waiting for Judith Mossman's signal. Alyx Vance and Gordon Freeman separately escape the attack.
Because the Combine don't have Freeman, Mossman's deal for Eli's safety is off, so the Combine capture Eli Vance and take him to Nova Prospekt. Judith Mossman is taken too.
Freeman escapes through the Ravenholm tunnel. Aided by Father Grigori, who is now insane, Freeman spends the night fighting his way through Ravenholm and the Ravenholm mine. He reaches the surface near the coast at dawn the following day.
|Red Letter Day + 1
Freeman reaches the surface near a resistance base which is under attack. The resistance supplies him with a dune buggy and Freeman spends the day negotiating the coast road connecting Ravenholm to Nova Prospekt, overcoming Combine ambushes and defending resistance bases from attack the entire way. He arrives at Nova Prospekt at dusk.
|Night of RLD+1
Freeman and Alyx independently assault and penetrate the Nova Prospekt facility in an attempt to rescue Eli and Mossman. They meet up inside the facility and discover that Mossman is still walking around freely due to her (slight) betrayal, and still trying to bargain for Eli's life.
Mossman sets up the Combine's Nova Prospekt portal to emulate the human science team's "Xen relay" - which the Combine have not discovered, remember - and escapes through it to the Citadel, taking Eli with her. Alyx quickly restarts the portal and she and Freeman use it to escape. The portal explodes as they 'port out, with the result that Alyx and Freeman are sent on a "slow teleport" journey which will take over a week to complete.
The explosion of the Combine portal makes it impossible for more Combine forces to be dispatched to City 17. This, coupled with Alyx and Freeman being presumed KIA, is taken as a signal for the human resistance to begin its uprising against the Combine.
|A few days later
Dog makes it back to Kleiner's lab from Black Mesa East.
|Red Letter Day + 8
Alyx Vance and Gordon Freeman arrive at Kleiner's lab after their "slow teleport" journey. Their journey was subjectively instantaneous.
Alyx and Freeman join Barney Calhoun, Dog and many others in the assault on the Combine Citadel. Alyx is captured by the Combine. That evening, the Citadel is reached. Dog provides Freeman with a route through the "walking walls" and into the Citadel core.
|Evening of RLD+8
Gordon Freeman infiltrates the Combine Citadel but is himself captured, along with Eli and Alyx.
Breen tries to make Eli tell the resistance to stand down and let the Combine win. Eli refuses. Breen suggests installing Freeman as the leader of the resistance instead, if he will deliver the message instead.
Mossman redeems herself by intervening to save Eli. Alyx, Eli and Freeman are freed, while Breen escapes.
Breen attempts to transfer himself into a host body and escape through a Combine portal to another universe. Freeman destroys the portal, destabilising the Citadel's teleport core and causing it to detonate. The detonation has a knock-on effect on the other Citadels. Earth's connection to the Combine universe is severed.
The G-Man again retrieves Gordon Freeman - and possibly Alyx too - and places him into storage for future reference. However, vortigaunts intervene, forcibly removing Gordon Freeman and Alyx Vance from the G-Man's control and spiriting them away.
Breen also escapes the detonation. His mind is transferred into the host body of a Combine Advisor.
Meanwhile, Eli and Mossman escape the Citadel, presumably via Razor Train. Eli returns to Kleiner's lab while Mossman sets off on another task entirely.
|Night of RLD+8
By this time the detonation of the teleport core at the top of the Citadel is complete, and a great deal of destroyed Citadel has fallen into the city below. In addition, the Combine anti-antlion field has collapsed, allowing antlions to begin burrowing into City 17. The human reproductive suppression field has also collapsed. However, the Citadel itself is still intact for the moment.
Severed from the Combine universe, Combine forces arrange for the Citadel reactor - this time referring to the much larger reactor housed deep underground below the building - to overload. The result will be a colossal "dark energy flare" which is powerful enough to transmit a single packet of information through to the Combine universe... and incidentally completely destroy City 17. Isaac Kleiner and others reactivate as much local transportation as possible so that the city can be evacuated, and broadcast an announcment outlining these facts to the citizens.
Both Freeman and Vance are teleported by vortigaunts to the rubble immediately below the Citadel. Alyx recovers first, possibly having been discovered and rescued by Dog, who has been waiting outside since helping Freeman enter the Citadel earlier that day. She and Dog then uncover Freeman.
They restore contact with Eli Vance and Isaac Kleiner who inform them about the flare, which they presume to be an accidental result of the damage done to the Citadel. Dog helps them re-enter the Citadel.
While moving through the highly unstable Citadel, Freeman and Vance encounter a recording of Breen agreeing to be placed in a host body. Then, a life-support pod containing a live Combine Advisor inflicts them with powerful mind-blasts before jetting away.
Soon after, Vance uncovers evidence that the reactor overload is intentional, not accidental, and retrieves a copy of the content of the data packet that the Combine intended to send, though she cannot read it.
By this time, Mossman has located the site of the Borealis and sent back some video-- however, the Combine have caught up with her.
Vance retrieves this video too, while Freeman stabilises the reactor. The two attempt to escape via Razor Train. However, the train derails and they continue their evacuation of City 17 on foot. As they do so, the Combine restart the reactor overload procedure. The heroes have bought a few hours, but that is all.
|Red Letter Day + 9
Vance and Freeman fight their way through an antlion-infested underground parking structure and reach the surface early in the morning. They spend much of the day working their way through the remaining Combine forces in City 17, catching up with Barney Calhoun in the process. All three escape the city by conventional rail.
As Vance and Freeman are leaving the city, pods containing Combine Advisors are jettisoned from the Citadel and across the surrounding countryside, inflicting them with mind-blasts as they pass overhead. The Combine dark energy flare is triggered. The mysterious data packet is sent home to the Combine universe, and the Citadel detonates, completely destroying City 17 and everybody left within the city limits, and once again derailing Vance and Freeman's train.
|to be added: Episode Two
"Ratman" is woken up by GLaDOS and led through the Aperture Science Enrichment Center Test Chambers. He gets as far as Test Chamber 17 or so, but is unable to solve the puzzle, goes mad, hallucinates that the Weighted Companion Cube is talking to him, and escapes the test chambers via Chamber 16, scrawling "THE CAKE IS A LIE" and other helpful directions on the walls on his way out.
Among the things Ratman has scrawled on the wall is the CJOHNSON/TIER3 username/password for use on the Aperture Science website - or rather, within the Half-Life universe, on the Aperture computer terminals.
Chell is woken up by GLaDOS and solves all the Aperture Science Test Chambers. She escapes into the "backstage" area of the facility, confronts and shuts down GLaDOS. In the ensuing explosion, Chell is jettisoned to the surface outside the facility and falls unconscious. She is taken back inside the facility by a robot and placed into cryogenic storage.
Ratman, with his beloved Weighted Companion Cube in tow, observes Chell's progress.
|to be added: Portal 2
Quite a lot of conjecture relating to the Portal universe has had to be thrown out in light of the Portal 2 prequel comic and Portal 2 itself. The following is no longer believed to be true:
This seems like a great pity since these all worked really well in the context of Portal alone. But oh well.