Didn't aperture's LIVE personell completely leave? According to what i read in their files, (site...duh.) my guess is that they started assembling GLaDOS as their assistant, when they activated her, it was "Bring-Your-Daughter to Work Day" (not kidding, it was.) and that someone's daughter was the character you play is in portal, and she was placed in the stasis chamber and GLaDOS flooded the lab with the neurotoxin, all of the other scientists died, I have no clue how the "Morality Core" got on GLaDOS, but in any case, whoever's daughter it was gets out, does the tests, escapes death, and destroys GLaDOS. About the morality core, my guess is that when she was flooding the neurotoxin, someone was already in there, and they got it on when the flood was completed, so he died. I think this because when you walk into GLaDOS' room in the last level, the morality core simply falls off, so it may have been put on in a hurry. (like i said...a huge part of it is my guess, some of it is info from the site.)

Curses, foiled again!