Yes, Half-Life 3 was once real. Sadly, the long fabled third entry in Valve's sci-fi epic never saw the light of day and we've all been lingering on that damn cliffhanger for about a decade. We'll probably never ever get answers to what happens next in Gordon Freeman's adventure… at least in a playable form.
Former Valve writer Marc Laidlaw just posted the plot of Half-Life 3 for you to gawk at since his NDA has expired and well, the company's 21st anniversary just happened. His personal blog post with the plot has been taken down but most of the names and some specific details were changed for copyright reasons (or something along those lines) so someone took to Pastebin to fill in the blanks.
In case you're too lazy to read the full plot (it's just a lengthy summary, not a script or anything) or find some of a it a bit confusing, we'll summarize it even further.
After the death and funeral of Eli Vance, Alyx and Freeman went to locate the lost ship, known as the Borealis, in the frozen tundra. The location of the ship was provided to the two via Dr. Mossman, Eli's assistant. Their goal was not to seize it but to destroy it so it wouldn't fall into the hands of the Combine. The two boarded a seaplane to begin their expedition and a support team would follow shortly after.
The seaplane was eventually taken down mid-flight, leaving the two to wander the dangerously cold arctic environment in search of the Borealis. When they finally reached their destination, it would have been revealed that the Combine beat the two heroes to the Borealis and the evil army had set up a fortress around it.
Alyx and Freeman would've attempted to stealthy board the wrecked ship but upon closer inspection, they realized the Borealis was phasing in and out of existence, causing a holograph-like appearance. The coordinates were not the exact location of the Borealis but a mere prediction of where it would end up appearing. The duo needed to time their infiltration onto the ship perfectly so they'd board it when it was fully physically in their location
Gordon and Alyx were eventually detained by the Combine before boarding the Borealis and met with a new version of Dr. Breen. The Combine backed up his consciousness into what is described as a "biological blank" and an "enormous grub". The new Breen would've been fearful of Freeman, not knowing that the real Breen was actually six feet under. Breen would've eventually admitted to Freeman and Alyx that he himself was a prisoner of the Combine and begged that the two would end his life, unable to stand living in his current form.
Laidlaw's summary notes that Freeman MIGHT have done something to help end Breen's suffering before proceeding, indicating it might be a choice given to the player. At some point, Alyx Vance and Gordon Freeman would've encountered Dr. Mossman who had been captured by the Combine. Alyx and Mossman got into a tense conversation where Alyx blamed her for the death of Eli and Mossman stated it was a sacrifice made for the mission at hand, she was a double agent. Freeman was willing to trust Mossman simply because she had gotten them this far.
After battling some Combine, Mossman tuned some frequencies so that the Borealis would stay in position for them to board it. The group rushed for the ship, fleeing Combine soldiers as the Resistance arrived and stayed back to keep them off of our heroes.
As they attempted to gain control of the ship, they discovered that the folks back at Aperture Science had been developing something called the Bootstrap Device. It would allow the ship and those aboard it to travel to any chosen location instantly. It had never been tested before and the crew that originally inhabited the ship found themselves in a terrible situation when the Combine arrived on Earth.
In a final act of desperation to hide a major breakthrough in science, the Borealis crew attempted to hide the ship in a place they thought no one would find it – Antarctica. Laidlaw went on to describe the ship as an entity that could occupy space in different parts of time. This means that the ship was almost a vessel to travel back in time to its original location on Lake Huron during the start of the Seven Hour War.
The group was able to see the Combine forces arriving at Aperture Science's labs while also seeing them in the Arctic battlefield outside the ship and even potentially glimpses of the future. During their moment of confusion and trying to process what they were witnessing, they debated on what they should do with the Borealis. Destroy it or save it by crashing it and firmly planting it in the ground so the Resistance could research it. Mossman wanted to save it while Alyx was keen on honoring her father's last wish to destroy it.
The two got into a heated fight which eventually leads to Mossman overpowering Alyx to take control of the ship and then… a gunshot. Alyx had shot Mossman dead. Alyx had hatched a plan to use the ship as a bomb that would plow into the Combine's fortress.
As the plan unfolded, a figure would've appeared out of seemingly nowhere. “Come along with me now, we’ve places to do and things to be,” said the figure known only as the G-Man. Yes, the entity that has haunted you throughout this damned series would've obviously returned but this time, with a twist. Alyx could see him. The words the G-Man spoke were not directed at Gordon Freeman, they were directed at Alyx. Alyx followed through some opening in space and time, leaving our only other hero alone… on a speeding ship that's nothing but a time bomb that will lead to his inevitable doom.
The ship explodes, destroying all of the scientific wonders that Aperture had created as well as Gordon himself. Well, that would have happened if not for the Vortigaunts. The creatures managed to save Gordon just in time and "plucked" him out of the Borealis and set him aside somewhere else in the world.
The rest of the summary is vague. It sounds as if Freeman lands in the far future. "Enough time has passed that few remember me, or what I was saying when last I spoke, or what precisely we hoped to accomplish. At this point, the resistance will have failed or succeeded, no thanks to me." Laidlaw writes from Freeman's perspective. "Old friends have been silenced, or fallen by the wayside. I no longer know or recognize most members of the research team, though I believe the spirit of rebellion still persists. I expect you know better than I the appropriate course of action, and I leave you to it. Expect no further correspondence from me regarding these matters; this is my final epistle." These are the final words of the summary.
It's closed out with Gordon Freeman signing off and that's all there is. We no longer have to wonder, folks.
That is the story of Half-Life 3.