I cannot stress enough that you should actually watch it, its a wild ride, but if you really don't want to, or just want to see the important parts presented to you, lovingly, here's a list of things to keep in mind over the course of HL2VRAI.
There is only one player, throughout the series. Gordon (thought that's not his name)
Gnome has the ability to mute NPC's, this could be part of why Al?x doesn't speak.
this ones kinda obvious but the player is not Wayne, though Baalup is kinda a character.
The process of turning off the game is painful in some way for the AI's, this was said by one of Coomer's clones, but it's worth repeating. I'm pretty sure this will have plot implications from here on out.
Benrey supposedly has a brother named Emmett. I say supposedly, because he is only mentioned by the Gnome once, and by Holly in The Chronicles of Benrey, which seems to me to be mostly a bit. (i dont feel this way about Scorpy's Chronicles, which I may get into in another post.
These games are really this universes versions of Half Life, however, for some reason, the player (who im just gonna call Gordon from now on because we don't know his real name yet) is the only one who has experienced these anomalies.
Gordon genuinely views the AI's as his friends, particularly Gnome and Dr. Coomer.
He also understands that they are sentient (although everyone else thinks he's insane)
In the final three episodes there is a "directors commentary" that confesses to three things.
The first, that Valve was fully aware that the game was sentient and, as I'll explain later, can effect the real world.
The second, is that parts of the game's code was etched into some freaky ancient tablet.
The "directors commentary" finally confesses that he has no idea how some of the NPCs came into the game. The one he names being Gnome.
Now I have to talk about Peppa Pig.
Peppa Pig (i wont explain it, watch the video it's five minutes and batshit insane) tells Gordon several important things.
There are three sentient entities (possibly not originally from the code) in the game. Gnome, "The Man in Blue" (Benrey), and "The Girl" who most people believe to be Al?x.
These entities are able to see and hear things outside of human capabilities, but not without damaging them. This may be another part of the reason Al?x does not speak, and possibly (though, this is conjecture) why Benrey is so distracted and incongruent throughout HLVRAI.
These entities (or at least, Gnome) are capable of entering the real world. and trapping players (or maybe just Gordon. Unclear) in the code of the game.
The entities are not entirely malicious however. Gnome feels immense guilt for this almost immediately and lets Gordon out. Not before the longest, most most ear grating song ever.
Some of these are interpretations, but I tried to be as clear about what I thought was intended versus what was conjecture. Anything I said as explicate fact is clearly stated for the viewer or implicit within the text.