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If GLaDoS is caroline from the beginning, why are there corrupted cores? and why is there even a core replacement option if it was caroline all along?
I think Cave was one of the Cores but got corrupted, so they tested a few other cores till they perfected it and put caroline into a core as Glados.
Thus to comment on the OP's theory, it would seem the psychotic part of Glados was already functioning during Bring your Daughter to Work Day (ie. Cave's brain had been successfully save to disc, but whether he was dead or not is unknown). We don't know exactly when they tried installing the morality part (nor whether the process of having her brain saved to disc resulted in Caroline's death or not). All we know is that the installation failed to bring Glados under control.
1. Caroline maybe agreed. A lot of time passed, and now they figured out how could they put someone on a computer. Caroline was dieing because she was old or hurt. And they just put her on the computer (GLaDOS).
2. Caroline doesnt wanted to run it. Than after a while, when they figured out how to do it, they put Caroline into a computer. But she still doesnt wanted to test, thats why they put a little bit of Cave to the computer too.
I think the 2nd is more posibble, because i think in the 1st one, she wouldnt be so bad. Well, in the story, we dont know much about Caroline, but i think she wasnt a bad person.
And another thing. Im not sure that the other personal on that computer is Cave, but someone should be. Because, when GLaDOS said "Caroline deleted" Caroline was deleted, but something else should be on it. I can tell a lot of things about the story, because i know the whole storyline, and more important, the hidden or untold story parts. I think the untold storyline is even more longer. For example, in Portal 1, at the end, GLaDOS said "Black Mesa". And in Portal 2, what could we found at the old facility? Borailis... That unknown ship from Half Life 2 series. I think if there would be Portal 3, we could be sure that the Aperture Science and Black Mesa is connected. If you want me to tell more about it, add me to your friendlist.
-They found that Cave's brain being inserted was simply not enough to allow everything to properly function.
-They may have been unable to completley insert all of Cave's brain for one reason or another [maybe because of the disease he contracted...?] and as a result they inserted Caroline to either assist in allowing full capablities or simply as a back up prossecer
-Caroline was originally a backup, in case something went sour. Either Caroline wanted control anyway or -more likely- Cave somewhat failed, and Caroline was SUPPOSED to take over, but Cave's side wanted to remain in control despite being semi-inoperable, and as a result it could have been an internal fight that may have actually caused the whole faciluty to be killed to start with [either accidente or perhaps a threat carried by one half to try and convince the other to allow full control, but the second half did not believe this or complie, so the first half either carried it on].
Honestly a tough call here, and personally this brings up a second issue:
According to the Portal comics, GLaDOS attempted to use neuro-toxin everytime it was started up. Everytime however, she[?] was succesfully shut down. Eventually, she claimed to be calm and willing to work for scince, only wanting a little neuro-toxin to re-create an experiment. However, upon being fed the neruo-toxin, she immeditaly used it on the scientests, and only one escaped -along with Chell, somehow-, everyone else dying. However, in Portal, she is about to unleash a 'suprise', when suddenly a core falls out. Upon tossing it into the incenorator, she states it was meant to limit or entirerly PREVENT use of neuro-toxin, being installed by the scientests themselves [and it also allowed control over the rockets, but eh...].
As such, if there WAS a neruo-toxin core, how did she kill the scientests? And it takes Chell a full five minuties before it actually kills her, suggesting that it needs to reach certain levels before becoming lethal [sort of like radiation]. However, the comic states that it was going to pretty much kill you just seconds after inhailing it. So, what is the real cause here?