Crazy Theories
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So, this post is full of crazy theories. The post is just the beginning. Together we will dig into the truth, I think. First, let's agree that you have completed the single-player part of the game, okay? Otherwise, it would be unfair for you to argue or propose anything.

To begin with, let's analyze the well-known facts. What have we learned after completing Portal 1-2 and reading the comic?

  1. Cave Johnson is the founder of Aperture.

  2. Aperture was founded in the mid-20th century.

  3. Caroline is Cave's main assistant.

  4. Cave asked to preserve Caroline's mind. It was placed in a computer, and GLaDOS was created.

  5. Ratman spent several years in the Aperture laboratories. He initially worked there, then became a test subject, and later a fugitive. He saw Chell during the events of Portal 1.

Questions that arise:

  1. Why did Ratman put Chell at the top of the test subjects list when he was still young?

  2. Is Chell a clone?

Theories:

  1. Chell was in Aperture during her school years. She was placed in the capsule (the chamber at the beginning of Portal 1) only once during childhood. Most likely only once. I think Ratman, being young, found out there was a child in the capsule and, not wanting her to linger there, put her first in line (a moment from the comic). But Chell woke up only a few years later.

On the very first page of the comic, we see this:

Teddy Bear

Only little girls play with teddy bears. But in Portal 2, there was 100% proof that Chell was in Aperture during her childhood. Here’s a screenshot from chapter 5 - Escape.

Chell was a child; her parents brought her to work (Aperture).

Her parents (foster or biological - unknown) worked at Aperture! Even if we disregard the theory that Chell spent several years there, Chell was definitely in Aperture during her childhood, that’s indisputable.

  1. Cave Johnson and Caroline are family.

I’m trying to explain. You know the portrait? If I'm not mistaken and my sources are correct, in those times it wasn’t customary to paint oil portraits of strangers. A few people in an oil portrait are family members. Conclusion - in his last years, Cave married Caroline. The evidence is flimsy, I know, but that's what a theory is.

  1. The craziest theory for which I can't find proof. But if this theory is proven, I’ll be ready to die for Valve's genius.

Chell is the daughter of Cave and Caroline.

Doesn't the main character look like them?

The words of the final song seem like a subtle hint:

She was just like you,

(Although, maybe not as fat.)

Now Caroline is with us.

Chell's last name was not shown in the comic. Why? Because she is Johnson. Chell Johnson. If it had been written, the whole meaning of the riddles would have been lost.

Cave Johnson

Caroline Johnson

Chell Johnson

  1. A new theory based on the 3rd one. I completely forgot that both Wheatley and GLaDOS talked about adoption. What if Cave didn’t want a child? A sexual relationship and accidental pregnancy? Well, look. Cave was ill in his last years. He must have loved Caroline. But he didn’t want the child. Cave knew he couldn’t take care of a child. Maybe he refused to have the child and asked Caroline to refuse as well. Cave died, Chell was adopted. And later Caroline died too. Perhaps that’s why Chell's last name is [Modified] in the comic. If she was adopted by the Aperture employees, then she must have spent her entire life there since birth. And all three theories are covered by this one. :3

Updated

An addition to theory 4. GLaDOS said she found 2 relatives of Chell: a man and a woman. Foster parents? Did they also get tested?

An addition to theory 1. I found a screenshot with Cave and a little girl in the Final Hours of Portal 2.

Little Chell?

Translated the turret song!

My dear, beautiful dear.

My child between respect and evaluation.

My sweet, goodbye!

My dear girl, why don’t you stay away from science?

My dear dear girl.

I love you.

I cherish you.

I care for you.

Dear, I care for you.

Whose words? GLaDOS? Caroline? One of them. They wouldn’t just play a song with the words "goodbye my girl" without reason.

An addition to theory 3.

Chell or Caroline?

If it's Caroline, then the resemblance to Chell is incredible, leading to the conclusion that Chell is her daughter.

If it’s Chell, then the theory that Chell spent her childhood in the capsule is dismissed. And the question arises: did Chell really work at Aperture? If so, why is she being tested? In general, I feel that it’s not Chell. I don’t believe it, I don’t want to; then I’d have to build the whole puzzle anew. =\

Feel free to propose any theories and hypotheses in the comments, and we’ll discuss. Questions will be added to the post, and of course, revelations as well.