You start out a nameless test subject (Chell) that has been stripped of all person-hood (mute and suffering from amnesia). She awakes from stasis and after briefly confusion and aimlessness, is forced to complete test after test against her will. After realizing that it's this forever, until death, or trying to escape, Chell follows obscure clues and directions left behind by some other survivor. Evidenced by many 'nests' of hoarded food and supplies, they probably lived the remainder of their days crawling through the walls, on the run. Just how many subjects had been tested before her?
Eventually Chell manages to find and defeat the evil AI overmind (GLaDOS) that killed everyone in the facility with neurotoxin, who knows how long ago exactly, on Take Your Daughter to Work Day. How nefarious and curious. Why though? Is it just a case of an AI doing what an AI will inevitably do? Find humans meaningless? Is there more to this story than a lab rat wanting to be free? If you pay close attention, yeah, probably. Though the protagonist herself is in the dark.
As you play, you discover that Aperture Science was in direct competition with Black Mesa and, through no fault of its own, could not compete. Genius proprietor Cave Johnson slowly descends into madness the longer he tries to one-up his competition. To the point where he goes from working with the world's elite for the scientific advancement of mankind, Olympic athletes and astronauts, to basically conning homeless people into taking part in his experiments which get crazier and more desperate as years pass. Finally Apreture is bankrupt and, morally, so is Johnson. His ever loyal assistant Caroline remains by his side, and is in all likelihood the only one to do so.
Through gameplay and after the closing credits, it's easily concluded that during these earlier years Johnson and Caroline had a relationship deeper than business and, in all likelihood, had a child together. This child is adopted out to another scientist at the facility (evidenced by all of commentary about Chell being an orphan/adopted) for whatever reason, possibly against Caroline's wishes -- as you soon discover during this time period she is also forcibly uploaded into the system to become GLaDOS, a program/entity meant to oversee operations at the facility. That Caroline is Chell's mother is common conjecture at this point.
What seems less considered is why GLaDOS went rogue in the first place. Many seem to think that, as an AI, simply having her humanity removed did something that left her irrevocably evil and that's why she killed everyone. However, I doubt her motives were so shallow. Nothing about this series is that simple.
All seems to be going relatively well, after some tweaking to weed out problem behavior (probably because Caroline did not want to be there), until Take Your Daughter to Work Day. If you paid close attention to the dioramas set up by the children on that day, you'll notice that one of them is none other than Chell's. Meaning Chell was a child at the facility at the time of the neurotoxin event and in all likelihood grew up trapped within the facility. If you read her project, it also implies that Chell had no idea Johnson may've been her father and probably thought that her mother had died in labor, since there's no mention of a maternal figure at all.
Is it possible that GLaDOS went berserk after seeing her daughter again? A daughter she may not have wanted to give up in the first place? Were there other plans for Chell that GLaDOS, as overseer of the facility, became aware of and decided perpetual stasis was a more merciful fate? A way for them to be together at last, perhaps? Until tampering and/or system decay lead GLaDOS to forget all about being Caroline, about her daughter.
Upon rediscovering Caroline, GLaDOS appears regretful, and not only saves Chell from imminent demise at the hands of another, but also spares her when she has the opportunity to kill her herself. Which is allegedly all GLaDOS has ever wanted since meeting her. GLaDOS claims to delete Caroline, but during the credits sings about Caroline being there with her. There is no reason for GLaDOS to let Chell walk away. She says killing her is hard, but she had her surrounded and completely at her mercy when she says that. Perhaps she did not mean physically hard but rather emotionally so. Which is supported by the opera sung by the turrets as Chell ascends to the surface -- filled with flowery lyrics of endearment and love in Latin.
Once Caroline is reintegrated, are the continued jabs an attempt to encourage Chell to leave when she has the chance? It seems that, after this event, GLaDOS wants Chell to be free of all of this. That she is being driven away. Realizing that if Chell stayed, her programming -- to make humans test until they can't anymore, would trump any familial instincts that remained. Furthermore, if Chell knew, would she stay? If she had any inkling would leaving be harder? GLaDOS can't take that chance, and, right until the end maintains the charade that Caroline has been deleted and that Chell is loathed: nothing but a thorn in her proverbial side. But it's all a rather obvious ruse to the player, who is privvy (if they've been paying attention) to more information than Chell.
So instead of just a story about a Science Facility murdered by an evil AI that then proceeds to go through all of the humans in stasis to force them into testing for its amusement until they cannot test anymore... evil for evil's sake, you have something much cooler. A man being slowly destroyed by his work, descending into a desperate madness so dark that he kills the woman he loves (for science!) and can't bare to raise their child (or at least cannot raise her and use her for experiments, so he has to choose one or the other and he, of course, chooses science) so she's given to a fellow scientist. But despite best efforts Caroline's maternal instinct isn't easy to wipe clean and discovering the truth leads her to believe that Chell is better off dead -- and anyone else in the facility deserves to die for their part in all of this. Who knows what Johnson had planned for Chell, given what he had planned for Caroline.
Things confirmed as canon:
- Chell is an orphan, adopted by a scientist at Aperture Science.
- Chell was a child during The Event and completed a potato battery diorama.
- Aperture Science and Black Mesa are contemporaries and were in direct competition.
- Black Mesa's success is, at least in part, due to stealing technology from Aperture Science.
- Black Mesa is therefor partially responsible for the events at Aperture Science.
- Cave Johnson is a genius who is driven mad by his inability to succeed.
- In an effort to stay afloat his experiments become more dangerous and farfetched.
- Caroline is Johnson's assistant. Their relationship is a close one.
- Caroline stays by Johnson's side even as his company falls apart.
- Caroline becomes GLaDOS. This happens against her will.
- In order to control GLaDOS, they have to delete core aspects of Caroline's personality.
- They still cannot control GLaDOS.
- During Take Your Daughter to Work Day, GLaDOS locks down the facility and murders all of the people inside.
- Caroline and Chell are said to be very much alike. Both described as overly tenacious.
- Once Caroline is restored, GLaDOS' demeanor and attitude toward Chell change.
- When Chell's life is endangered by someone/thing else, GLaDOS saves her.
- When put at her mercy, GLaDOS doesn't kill Chell despite claiming that has been all she's wanted since their first encounter.
- GLaDOS claims to have deleted Caroline, but evidence suggests otherwise.