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Just two things I didn't get even after the end. Warning, plot spoilers ahead.
1. GLaDOS said she killed everyone in the facility with a deadly neuro toxin and that because of that, people installed a moral inhancer thingy module into her so that wouldn't happen again. So... they just installed the thing and left again or what?
2. What's the purpose of having someone go through a training course and then sending them into a fire? Since the firepit looked like it was supposed to be there I'd assume it was already built into the facility before everyone was killed. Why on earth?!
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Spoilers, again.
1. According to aperturescience.com, GLaDOS was hastily activated on "bring your daughter to work" day as a tech demo. According to GLaDOS her/itself, she/it proceeded to activate the neurotoxin, killing everyone inside. However, the scientists had six minutes (remember, the toxin took six minutes to activate) to install the "morality" core in an attempt to halt the process. Apparently, they didn't succeed, only installing it partially, and everyone still died. Partial installation also explains why the morality core just... kinda...
falls out of GLaDOS when you meet her.
The main character is Chell Johnson (see credits). She is the daughter of Cave Johnson, the CEO of Aperture Science. She was at the enrichment center the day GLaDOS was activated (take your daughter to work day). Apparently, she had agreed to be one of the test subjects in her father's portal project; the test subjects were kept alive in their "relaxation vaults" while the neurotoxin killed everyone else. Taking all of this into consideration, the following quote, which seems innocent when you first hear it, becomes much more sinister.
GLaDOS: "Remember! Take your daughter to work day is the perfect time to have her...
tested."
2. The fire pit looked broken out of the floor to me, as if it weren't originally there. GLaDOS was just disposing of the main character after she/it was done with her.