If you didn't make this connection immediately, there are some hints peppered throughout the game. Most obviously, the part where Cave's pre-recorded message says: "I'm going to burn your house down! With the lemons. I'm going to get my engineers to invent a combustible lemon that burns your house down." GLaDOS gets very excited by this and even remarks, "Burning people! He says what we all are thinking!" Cave is expressing the very desires of GLaDOS' heart. Or emotion chip. This suggests that GLaDOS and Cave have incredibly similar (if not exactly the same) thought processes.
The little bit we do learn of Caroline throughout the game points to a Caroline that is submissive and a bit slow-witted. (Cave: "Say goodbye, Caroline." Caroline: "Goodbye Caroline.") She doesn't have the extremely strong-willed nature or snappy wittiness that makes GLaDOS such an interesting adversary.
During one part of the Cave Johnson recordings, Caroline answers, "Yes sir, Mr. Johnson." GLaDOS says this at almost the exact same time. Even though this seems to contradict my theory, GLaDOS is seriously freaked out by this reaction. She immediately says "Who's there?" This points to the fact that there is another personality there that is starting to come out. This personality is Caroline. This is the point in the game where GLaDOS starts to realize Caroline is able to take control from time to time, explaining why GLaDOS is so much nicer to Chell during the whole potato sequence.
But why are there two personalities in GLaDOS? Well, GLaDOS never only consisted of a single personality. If you remember defeating her in the first Portal, the first thing you had to do was to remove three Personality Spheres. These weren't GLaDOS, these were "add-ons" to GLaDOS. The boss fight in Portal 2 has you do just the opposite: add three Personality Spheres to Wheatley in order to corrupt him.
This is further explained in the Portal 2: Lab Rat web comic. In one flashback, Doug Rattman, a scientist with Aperture, is standing with a powered-down GLaDOS in the background. After a colleague mentions that "Artificial consciousness is the next frontier," Rattman claims, "But every time we turn it on, it takes a sixteenth of a picosecond before it tries to kill us." He's obviously referring to GLaDOS. In another flashback, a scientist is working on a Personality Sphere. He refers to it as "a conscience." Rattman is cynical that this won't work, because "You can always ignore your conscience." So basically, GLaDOS was trying to kill the scientists, so they created these Personality Spheres as add-ons in an attempt to keep her restrained. In fact, it's explained in Portal 2 that Wheatley was created for this very reason. However, as we all know, they didn't work. GLaDOS was strong-willed enough to ignore these personality add-ons.
So what is Caroline's role in all this? Well, she was Cave's assistant/secretary, and it's subtly suggested that the two of them probably had some sort of affair. Caroline is the one person that Cave seems to really care about. So when Cave became an AI (GLaDOS), and the AI became murderous, the scientists needed to calm this thing down. The way they did that: by getting Caroline's personality into a Personality Sphere and uploading it to GLaDOS. The Caroline persona was a part of GLaDOS since before the events of the first Portal, but GLaDOS was strong-willed enough to keep it repressed until she was removed from her body and only powered by a potato battery. At the end of the game, she is reconnected with her old body, and finally knowing that Caroline is there, she is able to delete this pesky personality for good.
So, GLaDOS is, in fact, Cave Johnson's preserved personality. The evidence, while subtle, speaks for itself. I promise you, the next time you play through Portal 2, this is all going to be incredibly obvious.
By Josh Wirtanen
*The views expressed within this article are solely the opinion of the author and do not express the views held by Cheat Code Central.*