Something about Gordon Freeman that's extremely fascinating is how he was basically forced into the "Messiah" role by complete accident. Dude was on his way to work, caught in an extremely awful lab accident, and he was just fighting for his life so brutally that he ended up taking down an entire army, making the other less capable or equipped scientists assign him as the one that would go in and take down the Nihilanth - I mean, they basically didn't have many other options, or at least not many better options at their disposal. The whole time he basically doesn't have much of a say in any of it, which means he was practically railroaded into becoming the G-Man's employee by pure circumstance.
Doesn't get any better in Half Life 2 either - the surviving Black Mesa staff have turned this man they potentially sent to die into a legend amongst the resistance movement. The Vortigaunts chant his name as they draw murals on the canal walls. The Lambda - a symbol of both the Lambda Labs but most notably the symbol on the HEV suit - now symbolizes liberation. Therefore, of course, the man who bears this symbol is the liberator. By the ending chapters of Half Life 2, Freeman commands entire squads of rebels, appointed the leader regardless of how good a tactician he actually is - if they die, they died for him, not because of him. As long as he gets to the Citadel and breaches it's wall, all those deaths would be worth it - once again, others send him into a near-inhospitable environment to take down a near-invincible threat.
I think that despite us being in control of Freeman for most of the series, the real protagonists of the story are the Vance family. Eli, too, was right at ground zero when the Resonance Cascade occurred. He is the leader of the Resistance. It's very possible that he's the one who spread word of Freeman throughout City 17. The fall of Nova Prospekt AND the Citadel occurred as a result of Eli's capture. In the Combine's eyes, the Vances are a threat equal to, if not greater than Freeman himself. That, and the Vances have something Freeman doesn't - agency. They're beyond the G-Man's control. They're beyond the Combine's control. Their actions are completely their own, with no third party to control every single step they take. Over the course of the Episodes, it feels as though the dynamic shifts, with Alyx becoming a much more vital figure. The Combine are specifically after her now, because she carries the code capable of disrupting the portal through which the Combine could send reinforcements and finally consume Earth.
In both the Epistle 3 script and in Half Life Alyx it ends with her basically taking Freeman's position under the G-Man's employ. She quite literally takes the role of the Main Character away from Gordon. This, of course, is nothing to envy, because it's been repeatedly shown that any character assuming this role in the series ends up being reduced to nothing but a pawn for those who control them. It's an extremely fascinating spin on the linear nature of the games, canonically acknowledging you're doing nothing but marching along a path someone else made for you. Despite being the one free man, you're not offered much of a choice.
The Combine Overwatch is so mindbogglingly erotic to me. Civil Protection suits connect directly to the mind, they link to an overpowering central consciousness, they reward compliance with sexual pleasure. I wouldn't survive under the Combine because I'd join the Metrocops out of desperation, unload a magazine into an Antlion Guard, and get the same response that I would to shoving a Hitachi Wand between my legs. I'd have Ellen McLain whispering in my ear about my compliance being rewarded and I would be unable to resist any order she gave me. Whatever you say, mommy. If I throw another grenade into a barnacle nest, will you do that thing where I can't feel my legs for the rest of the day?
"Ugugu Gordon's actions would've meant nothing! It was barely a hit to the combine"
Humanity achieved the first successful rebellion against the combine. Ever. It proved they weren't invincible and maybe, just maybe, it'll inspire other planets to stand up too. If the combine can be hurt then they can be killed.
A resistance is made of big and small actions, you cannot have a revolution without the smallest act of just saying "no, I refuse"
The most powerful ability exclusive to humanity in the Half Life/Portal shared universe is our ability to just throw bullshit at the wall and see what sticks. Aperture "OSHA are the devil" Science have managed to create completely safe interconnected points in space. The same company that turns people's blood into gasoline and shoves lions and humans into the same enclosed space for the vague concept of "Science". Meanwhile Black Mesa still has to use Xen as a crossing and their teleportation device requires an entire reactor with a village's worth of staff constantly maintaining it, just to end up having most of said staff abducted by onion-headed aliens. Even the resistance hasn't managed to create completely stable teleporters with a compressed Xen relay, meanwhile Aperture just went "oh dude let's shove a black hole into a non-waterproof gun" and have just created a teleportation method that just removes Xen from the equation entirely. Doesn't change the fact they bullshat so bad they basically got themselves gassed to death, but still.
The Resistance are a good example of this too. The Combine seem to have a complete set-in-stone thought process and understanding of science which meant they didn't even begin to explore local teleportation via Xen, meanwhile a group of random human mechanics and scientists have managed to cobble together at least two semi-functional local teleporters out of scrap metal and stolen Combine tech, to the point the All-Consuming Interdimensional Empire had to straight up copy their homework. And that isn't even the only time they seem to be taking human shit to just copy the blueprints.
They 100% just yoinked the entire damn car out of that garage just to take a crack at reverse-engineering the Tau Cannon attached to it. Even Resistance weaponry somehow manages to rival or at least stand equal to Combine tech - and we're talking improvised crossbows that shoot superheated rods of rebar at the target compared to high-tech rifles that can discharge orbs of pure dark energy. The collapse of the entire Citadel is basically set into motion as a result of a cobbled together Rebel device placed into extremely capable hands.
The events of the Portal games are a case of extremely elaborate machinelike planning versus pure human improvisation, with Chell's entire escape in the first game involving her simply weaseling her way through small cracks that GLaDOS missed while setting up her ambushes, eventually turning her own rocket turret against her to destroy her.
I suppose you could argue this falls flat in Portal 2 with Wheatley, but it's important to remember he's designed to be an utter idiot, so it's safe to say he wouldn't obsess over the larger picture like GLaDOS to the point where he fails to see the cracks. Yes, he's the one that breaks Chell out of the test chambers again, and yes, he's the one that came up with the sabotage plot - but it's important to note while he knows what to target in the sabotage, when we actually get there he doesn't quite know how to sabotage it, leaving Chell to figure it out on her own. She botches the Turret Quality Control Line with some minor guidance, but it's basically completely up to her to figure out how to cut off the Neurotoxin Supply. It's through her improvisation that Wheatley even manages to get into GLaDOS' chamber, tumbling through her neurotoxin vent and shattering the glass cage she trapped Chell inside of. It's through Chell's improvisation that the Core Transfer even occurs in the first place.
The script is flipped specifically when Wheatley takes charge, because oops - turns out a mind capable of focusing on the bigger picture might be pretty important when it comes to running an entire facility powered by it's own Reactor. Wheatley just completely zeroes in on his own personal pleasure, hacking up test chambers and the objects within them to try and figure out the easiest way to get his solution euphoria as quick as possible.
Still, something that's pretty interesting is that only Wheatley has ever managed to create a trap that's impossible to foresee and avoid, something GLaDOS has repeatedly failed to do to the point she ends up commending him. I believe this is because his way of thinking is a lot closer to Chell's compared to GLaDOS'. He puts up way more of a fight as the two run through the facility trying to get to him, seemingly improvising on the spot just like Chell has been over the course of the two games. Even his lair would be impossible to survive if it weren't for a single Conversion Gel pipe he somehow failed to notice and remove.
Whether in a laboratory deep beneath the soil or an alien tower tall enough to split the clouds, the ingenuity of even a single person is enough to topple a tower or destroy a supercomputer 3 times over.
Marc Laidlaw put what I'm trying to say into a single sentence when writing for the BreenGrub twitter account:
"With the TARDIS secured, the Combine now have more-or-less free roam over the Universe Multiverse. Humanity, and many other species are most likely doomed.."