Marc Laidlaw, the lead writer on Half-Life 2, has updated his blog with what could only be seen as the entire story of the unreleased Episode 3.
Laidlaw's post came out of nowhere. In it, the former Valve writer details everything he had in mind for the final episode.
We're not sure if this is how it was back in 2008, or if it's the final draft. Laidlaw was careful to change the names of all heroes, but anyone who read it instantly knew who it was talking about.
If you don't have time to read several paragraphs worth of plot for "Epistle 3", then you can read on below for a summary.
After the death of Eli Vance in Episode 2, the resistance bury him and find the strength to go on. Alyx and Freeman then quickly head to the Antarctic to destroy the Borealis. Another team would follow them on a different transport.
As it tends to happen, Freeman's plane crashes. After navigating the harsh blizzard and following the coordinates to the Borealis, the team instead comes upon a fortified installation that they believe was put there by the Combine. They would later realise that the Combine had built this structure to study the Borealis.
Freeman and Alyx soon realised that the coordinates was for where the Borealis was predicted to arrive, not its current location, seeing as the sub was phasing in and out of dimensions. After deciding to find a way to board it, the pair get detained by Dr. Wallace Breen, or more accurately, a grub carrying the consciousness of Breen.
The Breen-grub didn't know that the original Dr. Breen had died, and after a conversation with the pair, the grub asks them to end its life. Which they do. Soon after, they find Judith Mossman in a detention cell. This is where things quickly get nasty between Alyx and Judith, with the former blaming the latter for her father's death. Judith, for her part, maintains that she was a double agent working for the resistance all along.
Alyx wasn't convinced, but they all went ahead and headed towards the coordinates anyway, where Judith managed to bring the sub into this plane of existence long enough for them to board it, along with some Combine pursuers. During their time there, the group saw glimpses of different parts of the series' timeline. They learned that a research team had created a self-contained teleportation device called the Bootsrap.
This was years before the invasion, but when the Combine finally took over Earth's research facilities, the team decided to use the device in desperation to send the Borealis into the the most distant place they could target, which happened to be Antarctica. The Bootstrap device had actually travelled in time and space to reach the destination, which the scientists hadn't realised.
After seeing this revelation and others as they fought off the Combine forces on board, the group couldn't get a plan together. Judith argued that the sub must be delivered to the resistance, but Alyx was committed to honouring her father's demand of destroying it. Then after an altercation, Alyx killed Judith. Freeman and Alyx then steered the ship, now equipped with a time-travelling missile they had put together, into the heart of the Combine command centre.
Then the G-Man appeared to Alyx for the first time, whom we don't get to understand any more about by the end of the story, and Alyx followed him. As the sub was on its course of destruction, the Vortigaunts reached in and grabbed Freeman before impact, sending him into a future timeline. Freeman remarks that he doesn't recognise most members of the research team, and that a few still remember him.
Nothing gets concluded, though, and we don't even know what happened in this future. The origins of the G-Man, and the rest of the many unanswered questions remain just as confusing.
Now, we wait for Half-Life 3 to finally solve the mystery.