Have to admit, it feels refreshing doing this again, after all the destruction of pop culture scifi, with decade old IPs having their lore and characters thrown to the bin like they were nothing.
Before we continue, ye, spoilers. Play HL Alyx or watch a playthrough(like I did). If you did, there is an after credits scene, just in case you didn't know.
Also to be clear, these theories are mine and mine alone. Don't take them as gospel truth.
SPOILERS BEYOND THIS POINT
Lets take things from the beginning.
After 20 years in stasis, and the events of black mesa*, Gordon is freed by G-man to fulfill his "assignment". The place, City 17. The events of HL2 leads to the destruction of the citadel and the attempt of the combine to open a massive portal to earth and poor in. When Alyx asks G-man to take the combine off earth for freeing him(in half life Alyx's ending sequence) he says that this is too big a favor, considering his employers interests. So, at this point, it's probably safe to assume that this was G-man's intent.
*Based on Eli in ep2, G-man brought the crystal that caused the resonance cascade in black mesa. Therefore, that was undoubtedly G-man's plan.
Things go awry for G-man when the vorties intervened and freed Gordon in ep 1
It's at this point Gordon went off the path that G-man had laid before him. Gordon was never supposed to do what he did in ep 1 and then ep 2. Delaying the self destruction of the citadel and then closing the combine portal, effectively thwarting G-man's plan to, for whatever reason, bring the combine's full force to earth.* And he didn't stop, knowing that these were not G-man's plans
*In Half Life Alyx it is made pretty clear that the combine consider the G-man a threat. He also instigated Breen's death and the Citadel's destruction. So it is unlikely that he is somehow allied or otherwise affiliated with them, neither he is interested in them in overrunning earth's resistance.
At this point G-man "fired" Gordon, and he needed a replacement. And this brings us to the events of Alyx.
To recap the events of HL Alyx, it is 5 years before the events of HL2. In a quarantined zone of city 17 the combine find and capture G-man*. His imprisonment is so imperative that they capture him along with the building he is in and anyone having any knowledge of even the place is pretty much a dead man. Alyx went on a mission to destroy what she and Eli thought was a weapon, on the way there they find out it is a prison. Due do a dialogue between a combine advisor and who we can assume is Mossman our protagonists mistakenly decreed that Gordon must be held in there. When, after lots of trials and tribulations she finally enters the prison and frees G-man, he offers her the chance to save her father 5 years in the future from dying, by killing the advisor that had her father, and she does. But he takes her and puts her in stasis as a replacement to Gordon. After the credits end, we wake up as Gordon at the end of Ep2, with Eli pretty much alive, but with Alyx gone. Mind blown.
*It is unclear and it is never revealed how the combine manage to capture the G-man. Only two possibilities exist. He either went to the past to find a more suitable replacement to Gordon and the combine trapped him, or he got caught on purpose in order to wait for his "savior" as the candidate for hire. Interesting detail is that the combine are using vortigaunt power to hold him captive, which is in line with ep1, where Vorties hold him back in order to save Gordon.
So, what happened in HL Alyx? For starters it is here where time travel is confirmed in the half life universe. In the past it was merely theorized by fans that it was a thing. It is possible that Eli's death was G-man's plan to get Alyx in the past to act and save him. Then take her away. However it is still up in the air and G-man might have actually genuinely gave her the option to do it for freeing him. But it is shown that G-man is a manipulative individual. So I lean more on the "he did it to "hire" her" idea. Either way, He took her. But how, or even when? Well, I think that after the events of Alyx, G-man wiped her memory and send her back. 5 Years later, in white forest, the advisor gets zapped and fried in a dizzying flash out of nowhere, while Alyx disappears, setting up the events for ep3.
Some side Theories
G-man and his employers vs the combine? It is very likely that the combine are not the only galactic power out there. Perhaps they have enemies who want to take them out. What's certain, is that some form of monetary exchange is taking place and the combine's enemies pay well for the service of fighting the combine. Not only that, it's possible that there are other factions that want G-man's little peons of destruction for other conflicts or operations.
G-man and his employers are not infallible or all powerful. The Vorties are shown to be able to collectively deal with G-man. G-man is able to manipulate time and open portals anywhere. He is rather elusive and quite powerful, but he is not shown often engaging in time shenanigans. Being an employee(or a independent contractor maybe?), its quite possible that his employers are perhaps equal or more powerful. However needing to engage in agent insertion, employing lesser, albeit skilled beings, like Gordon, shows that their enemies(like the combine) are not slouches either. Probably using time manipulation could give you up to your enemies(maybe that's how G-man got captured). The moment before Alyx zapped the advisor, he turned his head to face us as if the advisor could see Alyx and even potentially G-man. Certainly, G-man's enemies have the countermeasures to deal with his and his employers' power.
Another theory, which I do not really like, is parallel dimensions. Basically Eli's death occurred in an alternate reality to the one where Alyx saves him, but this theory can't really stand, because G-man is shown to reverse and alter that very moment.
G-man is lying or what he tells us is to simplify incomprehensible events taking place. In this theory basically G-man has no employers, but he himself is that mastermind. Problem is, he has no reason to lie about it. However, another thing is that concepts like employment, payment etc might be simplifications of what is really events, intents and motivations which, much like G-man's true form, are beyond mere human understanding and comprehension. But I do not think that this would make an interesting plot.
So that is my take. What is yours?
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