guess it's been a long time coming at this point. supposedly, the non-disclosure agreement for half life 3 ended this year, and with that marc (storywriter for half-life just in case someone isn't familiar with him) went ahead and gave us a what looks to be a full (albeit coded) rundown of how the story was to go in the form of gordon freeman writing a letter to the player
link to his page with the story (website is experiencing downtime due to how much traffic it's getting):
http://www.marclaidlaw.com/epistle-3/pastebin which looks to have translated the coded storyline:
https://pastebin.com/q9DMFa7c