I want to know everything related to the story.
I just finished the story and I have so many questions. I've read Lab Rat before playing Portal 2, but there are still some thing I haven't understand (maybe because they are not explained at all, maybe because I didn't pay enough attention), so I open this topic in order to ask every question that come in my mind. Maybe if this becomes popular and there are more people asking, answering and generally discussing about possibilities, I'll edit this post and add every question together with the answer so that other users can find it easily.
I'll first ask what is in my mind right now, and add more as soon as I remember them.
To begin with, who is the guy in the comic? Obivously an Aperature employee but what happened exactly and why did he stay there? Where did he live and what was he waiting for? Why is he saying Chell is "the one" and what is the "hunch" in Chell's file he is talking about. Where did Chell come from? Was she a random person taking part in the tests or something more than that? Why was she the only one who survived all these years and what happened to the others? What is happened in humanity, because it makes it look like there's no one left. What year are the events happening in? Wheatley is a core; he was made to "add" morality to GlaDOS, but where was he before finding Chell and why did he do that? Cave was dead when Caroline's consiousness in GlaDOS?
Well, that is all for now, but I'm certainly going to ask more. Feel free to answer me with "conspiracies", meaning that there is no official explanation but only fans' opinion.
Edit: Didn't take long: What about Chell's legs?
From here starts the Q&A:
Q: What about Chell's legs?
A: She wears aperture long fall boots.
Q: Who is the guy in the comic? Obivously an Aperature employee but what happened exactly and why did he stay there? Where did he live and what was he waiting for?
A: The man in the comic is Doug Rattmann. He is a schizophrentic scientist that drew the murals in Portal 1 and 2. He's the one that left you all the messages scrawled on the walls throughout the game. He was one of the only survivors of the neurotoxin incident in which GLaDOS gassed the facility with neurotoxin, killing many of the scientists and capturing everyone else that remained--except for Doug Rattmann, who managed to stay away from her. He had to stay in the facility because he was trapped there until GLaDOS was finally "killed."
Q: Why is he saying Chell is "the one" and what is the "hunch" in Chell's file he is talking about?
A: Rattmann wanted Chell to be the one to take down GLaDOS. His "hunch" is seen at the end of the comic--we see Chell's file, where it's showed that she never gives up, ever, and should not be tested, hence why she's the perfect subject to take down GLaDOS. Unlike the other subjects, she would not give up even at the fire pit of chamber 19.
Q: Where did Chell come from? Was she a random person taking part in the tests or something more than that?
A: Chell's past is mysterious but it's hinted that she may have been a child brought in by one of the scientists on Bring Your Daughter to Work Day. If you recall the science experiments you come across in Chapter 5, there's one with a gigantic potato that Wheatley comments on. If you look at the card behind the potato, it shows that the project was Chell's. How she came to be a test subject is unknown.
Q: Why was she the only one who survived all these years and what happened to the others?
A: In the comic, we see that she is taken to the extended relaxation center--into a cryosleep chamber. When GLaDOS was killed, the cryosleep chambers were knocked offline, meaning she would have not been able to survive. Rattmann patched her into the emergency grid, bringing her chamber online and keeping her alive. Wheatley was watching over the cryosleep chambers for a while, but he did not do his job, and thus wound up letting many of the humans die in the offline chambers. He explains at the end of the game that six humans survived, and Chell was one of them. When the facility began to grow run down and the reactor was in danger of exploding (if you listen to him before letting him in at the beginning of the game, he explains that unless you help him, you'll both die), he knew he had to get out of there, and tried to get the surviving test subjects to help him. He tried to lead each of them to the portal gun, but they all died before they could reach it (possibly due to his incompetence). Chell was the only one who made it. There were, however, other humans that survived deep within Aperture in the human storage. The entire co-op plot is GLaDOS connecting herself to the rest of Aperture and using the co-op bots to reach the humans.
Q: What has happened in humanity, because it makes it look like there's no one left.
A: That... we're not sure. The Portal and Half-Life games take place in the same universe, so shortly after GLaDOS killed a bunch of the scientists and locked down the facility, the whole incident with the Combine happened. You'll have to play the Half-Life games to get a better idea for what happened there.
Q: What year are the events happening in?
A: GLaDOS was created sometime in the 90s I believe. But we don't know the exact time period between Portal 1 and 2.
Q: More information about Wheatley?
A: Wheatley was not made to add morality to GLaDOS--that was what the Morality Core was supposed to do. The cores were created in an attempt to leash GLaDOS so the scientists could control her. Wheatley was made to make her more stupid and easier to control. He, like most of the cores, failed in this, and was repurposed to work in other parts of Aperture. We learn through his dialogue that he tried to work in other places like manufacturing (though this job was given to another robot), and in a deleted line he explains he once worked as the "assistant-to-the-guy-in-charge-of-the-neurotoxin-button." In the beginning of Portal 2 we learn that he was supposed to be in charge of the humans in cryosleep, but did a pretty crappy job there. He also talked himself onto the nanobot work crew. It's possible that he could have bounced around between jobs. We really don't have anything to go off of other than what he explains.
Q: Cave was dead when Caroline's consiousness in GlaDOS?
A: Yes. Cave said that if he died before they could put his consciousness into a computer, Caroline would take his place. And since Caroline DID take his place, logic says that he did die before that happened.
Credits to BabyCharmander for her answers so far.