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Spoilers ahoy! I've heard a lot of speculation about the story and this seems to make the most sense to me.
Spoiler: GLaDOS is created to help improve the research being done so Aperture can compete with Black Mesa but she goes rogue and releases neurotoxins into the enrichment center. A morality core is installed to prevent that but she ends up closing off the center and trapping the humans inside to be tested. It's likely this happened on Bring your Daughter to Work day, and your character in Portal is one of the children who came along but is now grown up.
Humans are tested until a working portal gun is produced. A previous test subject, possible another daughter, goes through the tests but takes days or weeks or solve the puzzles hence the references to passing out from thirst, the hidden nooks and crannies with writing, food and water. Eventually she escapes the testing chambers but ends up dying before getting to GLaDOS.
GLaDOS is aware of the Combine invasion but does little about it. She constantly says she wants to stay inside, doesn't like the outside. She also sends the Borealis to a random spot to prevent the Combine from getting the portal technology. Aperture Science's portals are far superior to the Combine and Black Mesa versions, we all know what happened when Black Mesa created a portal right?
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The black wind howls...
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