To start it off, I tie in Portal to Half-Life 2!
Possible spoilers! wrote:Here's what I think happened, and I'll start with Portal, since we know what happens in HL1.
GLaDOS kills the majority of the Aperture Labs with her nerve gas. However, for the various test subjects before Chell, she puts through the various tests, one by one. However, they're all killed, some because of the tests, other, I believe, were executed, because they saw through GLaDOS's lies (Or perhaps caught her slipping up), and were executed, but not before leaving messages in hidden rooms. I also believe that they, too, were given the two halves of the Portal Gun, which, when they died, GLaDOS retrieved, cleaned up the bloodstains and bodies. (But, curiously enough, not the graffiti behind the walls)
While GLaDOS ran her morbid tests, Gordon Freeman kills the Nihilanth, thus triggering the portal storms, the Seven Hour War, and the subsequent enslavement of the human race. GLaDOS, sensing opportunity, handed over whatever Aperture technology she could to the Combine. (Such as the Aperture Plasma Ball, which the Combine use as both a power source like Aperture did, and as a weapon)
And here's my justification:
For the timeline: Various staff meeting rooms show a comparison of Aperture revenue and funding in comparison to Black Mesa. This shows that everyone was killed either during or before Resonance Cascade, because A) The Combine would probably not allow Aperture to develop anything, and B) Aperture would probably realize that they've been competing with a dead company. (Because Breen would probably have told them)
And for the technology: When you enter the first test with the Aperture Plasma Ball, probably the first thing you would notice is that it acts in the exact same manner to the Combine Plasma Ball. Plus, it's very likely GLaDOS would sell Aperture tech to the Combine, probably for the same reason she killed everyone in aperture/
And that's about that.