So, the last couple of days I've been digging into the different theories of portal.
This may or may not be an outdebated subject, but here goes none the less.
(This is my collection of theories with my own variations . If you have comments or critics of them please let me know! I'm looking to punch holes in it or to confirm that they're not all crazy)
So first of all.
GLADOS is Caroline. That is made quite clear throughout the game. Chell is Johnson and Caroline's daughter.
GLADOS realizes she is Caroline at the end of P2, which is why she has shown no regard for Chell's safety etc. before that.
When GLADOS says she deletes Caroline at the end of P2 she is lying. She still loves Chell and wants her to leave so that Chell can live a life in freedom, without being sorry for leaving her mother.
There has been speculations that the company cubes are filled with failed test subjects' remains. Whether the cube you incinerated in P1 and got back at the very end of P2 is Chells brother, sister or another relative I'm not sure what to think of.
Speaking of Rattmann.
I recently saw a video on youtube of the Borealis. In the video the narrator told, that it was discovered that Aperture and Black mesa "shared" two scientist. A woman and a black bearded and haired man. In the portal comic Rattmann is shown as being black haired, bearded and having Black mesa technology in his lab. Furthermore his manic rants from P2 have been analyzed as including something along the lines of him being taken to Black mesa.
The ship Aperture used for teleportation research. The ship disappeared without a trace from its drydock several miles below ground. Rattmann's rant mentions "the ship" and "it's stolen" so maybe the other double scientist (the woman I mentioned earlier) betrayed Aperture and tried to steal the ship to Black Mesa. How the ship ended up in the arctic is, as far as I know, unknown. Maybe something went wrong in the teleportation, maybe it was later transported there to be hidden from Aperture.
Whether Rattmann ever escaped Aperture I don't know, but I doubt it.
So. That's my cents on the subject. Please let me know what you think of it and shoot it down if you can! :)
I'm so looking forward for the third and final game in the half life series. I think they will finaly link the two games completely together, making it a smart double-trilogy as it would be both HLE3 and Portal 3.
I know I don't have any sources in my post. That's because I count on people to know most of the facts already. If there are any questions about the sources just ask, I'll provide them.