The Real Villain Of Portal 2 Is One You Didn't Even Suspect
Throughout these recordings, Cave blasts competing company Black Mesa for stealing his ideas and sabotaging his work, which always seems to rub Caroline the wrong way. In fact, she always attempts to redirect the conversation when these accusations are brought up and calm him down. Though initially it appears like this is purely for Cave's sake, who shouldn't be spending his final days stressing over what the competition may or may not be doing, Caroline does seem to be almost personally offended by the Black Mesa talk. Almost like she has some kind of connection to them.
One theory goes, then, that she was actually sent as a double agent to spy on Aperture Science and gain the trust of its key personnel. Not only that, but it's also hypothesised that it was her who actually poisoned Cave. Though he is supposedly succumbing to Moon Rock poisoning after testing the portal gun, that explanation kind of falls apart when Chel has been exposed to the same substance for years without, you know, dropping dead. Consequently, it’s implied that it’s something else that led to his illness. And who was the only person close to him who not only nobody would expect, but who could convince him that it was indeed the fault of the Moon Rock to begin with? Caroline.
Perhaps a more compelling reason to believe she was some sort of spy is that when Cave is near death, he attempts to achieve immortality by uploading his own consciousness to GLaDOS, which Caroline actually sabotages. Unfortunately for her, in the process she actually indirectly uploads her own consciousness to the project, creating the amalgamation everyone knows and loves today. If that's not incriminating enough, Caroline's own memory of working with Black Mesa may actually be visible in the first Portal game. In that, you can briefly see an image of the Black Mesa symbol on GLaDOS' screens, perhaps a fleeting memory resurfacing from the real Caroline.