This video explains how Half-Life: Alyx's ending changed what would have been Half-Life 3 and Epistle 3 is no longer going to be Half-Life 3
Epistle 3: https://www.marclaidlaw.com/epistle-3/
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Script:
On August 25th 2017, Marc Laidlaw, a former writer at Valve who helped write the Half-Life trilogy, posted an article on his website titled “Epistle 3.” This article will be in the description, and will not be summarized in this video, so go read it if you haven't already.
This article uses code names and code words for characters, objects, and more in the Half-Life franchise, and is very obviously the description and story of what happens in Half-Life 3.
but that was before the timeline was altered by the ending of Half-Life: Alyx, where Eli Vance is saved by Alyx’s past self. Her past self is then hired and put into stasis by the GMan.
this changes everything about Half-Life 3 that was in Epistle 3 and even known before the release of Half-life: Alyx.
Valve most likely changed the story because:
Valve loves to rewrite everything. Portal 2 was originally a completely different game where you played as a test subject named Mel during Aperture Science in the 80s, Valve redid the entire original Half-life game, and Team Fortress 2 was going to be more like Team Fortress classic where it was more of a military realistic styled shooter
And because Marc Laidlaw spoiled the original Half-life 3, they had to change that. And while Half-life: Alyx was in development, they had to slightly change the story. It's possible that what Alyx was trying to get out of that vault was actually a super weapon. Valve may have just changed the story so they could completely recreate Half-life 3’s story as well as concepts.
So Half-life 3 will not be Epistle 3. it will possibly be similar with all the things going on with the Borealis, but the story would change dramatically because Alyx won't be there, and Gordon and Eli will possibly have to defeat the GMan to get Alyx back, or the GMan may even make Gordon and Alyx fight each other. But there are 2 Alyx’s now. When the GMan took the past Alyx, he also took the Alyx from the end of Episode 2, which is shown in the post credits scene and implied by Eli during the same scene.
These are only theories. Do not expect them to be in Half-life 3, which will come out. Valve has said that because they now have the tools to do it, they can, and most likely will.
So thats why Half-life 3 will not be Epistle 3.