This is going to be pretty descriptive so bear with me. This is based off of a drawing done by Rattmann from the Final Hours of Portal 2. So Cryogenic freezing did occur, and clones would likely follow. And mutations etc. Just go with it. Cover-ups are kewl

All the frozen testers slumber.

There is a room in the deepest basement down the darkest stairs past the longest corridor at Aperture Laboratories.

Few know about it, fewer have seen it, and only the fewest have access to it.

Of all the inhumane human testing, and civil lawsuits, this topped them all.

In the Glory Days of Aperture, when test subjects included astronauts, Olympians and war heroes, there was no need for such a room. Success rates were high and the science was promising.

But it takes one public death to destroy that legacy. The 17th man on the moon happened to look into the handheld portal device.

The story broke, funding cut, and a severe lack of volunteers. Sure, civilians and homeless could do they trick, but they were stupid and petty with a horrible habit of dying. Robots just didn't provide the necessary results. When the employees started retaliating, there was panic in every inch of Cave Johnson's brain. He had to do something. Without initial human testing, this science would take decades before it would be useable.

That's when he mandated the genetic engineering.

And the Cryogenic freezing.

And the Cryogenic freezing of the genetically modified clones.

If it was good enough for Walt Disney, it was good enough for him.

The need for volunteers vanished, as the best and brightest scientists could simply grow another life, fixing the defect, or pull one out of the freezer.

By this point, everyone directly involved with testing knew about some more 'controversial' prerequisite testing procedures, but no one asked too many questions. It wasn't until they kept seeing the same face over and over again on the floor, despite being past the window of productive testing.

Rumors spread throughout the company, but no one really knew just what was going on.

Up in the fungal preservation wing in the curtain aspect of the company, a certain schizophrenic scientist was beginning to piece the story together. It took time but he did, but he could do nothing about it, for he was walking a fine line already with his illness.

He kept silent for two years until more whispers passed through.

Immortality

Cyborgs

Droids

Accelerated evolution

The same people who should have been dead from testing, still were. And no, people weren't getting better.

He put in a memo to meet with the CEO, and eventually was. When he confronted Johnson about the accusations, Cave was astonished. How did this get so public?

He wasn't too worried, as this young scientist accused him, they've faced worse before, but one question altered the inner workings of Aperture forever.

Is this testing for the device, or trying to remake the human race?

Cave got scared. He never thought of it like that. He shut the project down.

Down about three stories and up seven security levels. That was actually a brilliant idea.

Fewer people monitored testing, and more scientists were placed in the Curtain branch of the company.

The greatest minds vanished, and employees thought to testing, but really they were monitoring the gene bank of 75 subjects, and the walk-in Cryo freezer equipped to hold 5000.

The freezer was about half a mile long, and row after row and stack after stack of pods, each filled with multiple copies of the same subject.

The copies, once thawed, had no memories of anything past and were used in all types of new testing. Some more practical, others far fetched and sadistic.

This went on for another 25 years, and then Cave Johnson died, but the project lived. Barely.

Numbers were cut again, people 'relocated' and more secrecy added.

The tests got more and more violent and integrated with technology, up until the very day GLaDOS spiked the air with the neurotoxin created to kill the unneeded clones.

It wiped everyone. Except the 5000 in the air-tight pods. They lived.

And they slept. For years and years and years. They didn't feel it, or anything, and they didn't age, but they were still there. Still alive.

After Doug Rattmann survived, the first thing he did was look for all those people. They needed a chance to live, plus they could help him. But Doug didn't even know with what.

And he did. He found them. Through mile after mile of catwalks going nowhere, he found the hallway. The lock was broken, and he found himself in a lab. The lab.

There were two other doors. One looked like the door to a refrigerator, and the other was just a door. Obviously he needed the former, but still peeked through the other. In it, he saw the starting room for the standard tests. He knew because he has been through them, but he never started there. On the bed, was a subject (they weren't people anymore) with dark hair and skin. A female. A clipboard was next to the door and he found her name and number. Chell Jameson.

He heard about that scandal too. Cave would rather send his bastard child testing with a false (albeit bad) name than fess up to a relationship with his secretary.

He moved on to the freezer and opened the door. If his meds weren't wearing off before, he was seriously tripping now. The room was massive. The long, dimly lit hallway stretching as far as he can see.

Now he just has to unthaw them. He's a scientist. He can figure it out, right?

Of course not. And Doug begins to panic. He runs ahead down the hall, looking for anything that can help, and that's when he sees the bodies.

The Cryo doctors must've locked themselves in to escape the toxin, and then some tried to freeze themselves. No one succeeded. Petrified, Rattmann ran back the way he came and slammed the doors behind him. The way up and out was too long and far from here, but if he could get into the testing chambers, he could escape through the windows of the moderators. He ran into the waiting room and into the chamber.

"Well I'm glad someone survived."

xxx

"Quickly! Before she finds us!"

Wheatley and Chell raced along the catwalks, fearing GLaDOS would find them and ultimately kill them.

It seems like they're running for ages when they find a long spiral staircase going down.

As she dashes down three steps at a time, with Wheatley blabbering on in her ear, Chell can't think of much. She can't remember much, either. They finally reach the bottom of the vast staircase and find themselves in the dark. Wheatley turns on his flashlight and zooms a bit ahead Chell.

They keep running and running, for what feels like miles. Luckily, the long-fall boots are a bit springy, taking some of the strain off her legs, but Chell doesn't feel any burn whatsoever, despite the fact she has only woken hours ago and has run miles.

To her right, up ahead, Wheatley's light catches a glimmer of silver through an open door.

Wheatley makes no acknowledgement, but Chell looks in as she passes.

It's a lab with a large white and silver door, and both are open. Something is partially glowing white-blue from the silver door, and a flickering 01 sign protrudes from the other. It never strikes her as odd that see could see all that in one glimpse.

Wheatley catches her peeking and says something offhandedly about the nuclear reactor.

Chell keeps running for her life, and for her sanity.

From what she has seen, this factory is so massive; they have barely scratched the surface.

And she is alone. The last living human at Aperture, here and now is running from the murderous AI who can be credited for two destruction attempts of the corporation.

The odds are stacked against her, but Chell pushes it from her mind.

After all, she isn't really alone. And she will never be the last living being inside of Aperture.

5,000 subjects lost forever.

5,000 cursed to sleep forever and no one knows they ever even existed.

I love me a good Portal conspiracy.