Half Life: Full Life Consequences/WMG

In the time between Full Life Consequences 2 and Hero Beggining, John Freeman was working on portal technology.
John Freeman's attire at work suggests that he is a scientist. It is possible that he was working on portal technology, and put it to use to teleport himself to the melee at the end of Hero Beggining. The Combines either used similar technology of their own or stole it from the humens.

The pants are not dead. They are just sleeping.

 * Jossed in the Djy adaption of Free Man, as you see the pants floating up to heaven.
 * That doesn't make it canon!

Henry Freeman is not humen.
Gordon Freeman's last words imply that Henry Freeman is not humen, which could somehow explain his exceptional charisma. This also brings up the question of the entire Freeman lineage. If the family name wasn't a humen one, there is a lot more at stake than just living up to it. Which lends credence to the next point:

Humens are not humans.
The apparent misspelling of the word "human" is consistent throughout the Hero Beggining arc and doesn't happen in any other squirrelking stories. Henry Freeman's side of the family lives in a civilization of very similar beings to themselves. The Combines, knowing of the events in John Freeman's world, use portals to take Gordon Freeman's zombified body and not only bring it back to life, but conscript him with the "science" implants. On top of this, the Combines are apparently led by the Dark Man, who is implicitly not humen by virtue of his title as a "man" (he only looks like humen and Combine; perhaps he is some kind of amalgam powered by "science"?). John Freeman gives chase and sees Henry Freeman waging war on the Combines. Inspired by his progress, he decides to give his life to ensure humenkind's victory after failing to be of any service to mankind as well as his brother.
 * Didn't the Dark Man turn out to be ?
 * That depends on what adaptation you've been watching. It's not entirely clear in the text.
 * No, I got that impression from the original text. However, on closer inspection, it doesn't actually contradict the above theory. (There is plenty to go against John Freeman not being any good to mankind or Gordon Freeman. Maybe he was facing a different set of full-life consequences.)
 * Immediately after the dark man presses the button in Free Man, Gordon Freeman tells John Freeman about being stepped on by the next boss. It's entirely possible the author meant to reveal him as the Dark Man.

Henry Freeman is a demigod.
In Free Man, John calls out "Son and people get back!" What makes Henry different from the others? Simple: John is a god and Henry is a demigod. How else could they have defeated all the combines? How else could Henry have survived explosions the equivalent of 10 suns? How else could John be that unstoppable and awesome? In fact, the end of Free Man didn't even mention John being dead; it only says that John has a statue built in congratulations of him.
 * So John Ascended to A Higher Plane of Existence after his work on the physical world was done?

John Freeman is Ory'Hara
Based on the WMG from above, John Freeman IS the Universe and had to complete physical work by temporarily descending from the higher plane of existence

Wepon
In the same vein as the humans/humens distinction, wepon is a certain type of weapon that is particularly effective in disposing of the threats faced by the protagonists. In the first chapter, it's explained that John Freeman didn't have weapon. In the case of the headcrab officer, he could have wrestled the officer's gun off his person (as he no longer has any use for it) and shot him dead with it, then left it behind knowing it would be useless against the final boss. As Ravenholdm is the home of the sort of bosses that Gordon Freeman encounters, it would naturally have wepon in plentiful supply to the point where they litter the streets. These were the weapons used by whatever the zombie goasts used to be, but they were unfortunately overpowered by the bosses due to their lack of Freeman-like skills and rocket guns.
 * However, it still needs to be explained how the same cache of wepon made it to Henry Freeman's hometown for La Résistance to use.

John Freeman is a Time Lord
Gordon is really one of his regenerations, and his TARDIS is the car.

Henry Freeman's Mother
If the above points are true and humans are not humens, this means one of four things:
 * 1) Henry Freeman's mother is actually human and the Combines who killed her couldn't tell the difference.
 * 2) Henry Freeman's biological mother died and John Freeman married the humen girl during Henry Freeman's childhood.
 * 3) Henry Freeman was adopted.
 * 4) Henry Freeman is half-humen.

The full-life consequences John Freeman is so desperate to live up to refers to worldwide renown.
And he gets it in the form of a memorial statue.

John Freeman was transported forward in time just after the end of part 2
This might explain the apparent Time Skip and John Freeman's surprise appearance at the end of Hero Beggining; John Freeman was somehow sucked into a portal before he could fight Gordon Freeman, and during the time skip, the Combines came and Gordon Freeman got Combine science instead of the headcrab. Henry Freeman was probably alive before the timeskip and grew up while John Freeman was away; while neither he nor his mother are mentioned before Hero Beggining, there isn't any proof that they don't exist.
 * When the Combines arrived, presumably they used portals to get there. John Freeman was standing too close to the entrance point and accidentally got sucked into the future. The Combines didn't notice this, and with no one to stop them, the Combines put science in Gordon Freeman and used him to spearhead the takeover of the planet. John Freeman spent the time skip looking for his wife and son and got there in the heat of combat between the Combines and Henry Freeman's resistance.

Quarter-Life: Halfway To Destruction is a prequel.
It ends with Gordon getting captured. By the time John got to the bad place where Gordon was, Gordon broke free and was fighting the final bosss.
 * You're not the only one who thinks so.

John Freeman worked at a weapon manufacturer.
It's the only possible way he could have stockpiled so many arms in the second chapter. He was stuck in a desk job for years and Jumped At the Call when he got the best excuse to use their products. He was in a hurry the first time, but when he returned, he had the time to suit up and the knowledge of the next boss' weakness to rockets.

John Freeman was in stasis during the time skip, like Gordon Freeman in Half Life.
John Freeman was last seen right after Gordon was turned into zombie goast, so how did he get out? The answer is that the G-Man or someone teleported John Freeman out and kept him in stasis. During this time, Henry Freeman starts the rebellion. When they are about to lose, John Freeman is woken up and sent there to help.

It all takes place in The Matrix.
John Freeman is the first "The One", which would explain his superhuman (or superhumen) abilities.

The zombie goasts become the bots from the Satellite of Love.
In the Djy machinima, when they say "but this is our house :'(", it sounds too much like Crow to simply be a coincidence.

"squirrelking" is actually Gabe Newell.
He wrote the whole thing for fun, just like J.K. Rowling wrote My Immortal.

The 'Science' is some kind of substance.
How else could they put Science into Gordon Freeman to turn him from headcrab zombie to Dark Man?
 * In the Djy version, it seems to be some kind of robotic implant.

The entire story is being retold by people hundreds of years after the events happened
The bad grammar and spelling are because the spelling has changed over time, and because future humans adopted pidgin English.

The next boss was a Strider
It kills people by stepping on them and is weak to rockets. See the similarities?
 * ...Oh my god.

Forrest of time...
Is where the story takes place. John Freeman wanted the Combines to leave here, Forrest of Time, to keep his family safe.
 * Also, the city itself is called Freedome. Humens have to fight for it.
 * So it's a Domed Hometown, home of La Résistance and surrounded by the Lost Woods?

The humens were literally scarred
When Henry Freeman made them not scarred no no more, he healed their wounds with bear hands. This means that the Freeman family is possibly divine.
 * Jossed - Bear hands lower health.

John Freeman is a probably-divine Tennessee Walking Horse.
That's why he walks fast everywhere.

The rave sequence at the end of Free Man is John Freeman's afterlife.
In the beggining of the sequence, John wakes up in a blank white room, after being caught in the middle of the exploding tower. Then, his dead-once-more brother powerslides into the scene, transforming it into a mass of flashing lights, DJs, and most importantly, dead people. Over the course of the song, the now-handless bear, Wife, the Final Boss, the Engineer and others all make an appearance. This shows that this is the fate of everyone in the Full Life Consequences Universe: A totally kickass, post-mortem worldwide rave.