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It doesn't take an Aperture scientist to piece together that GLaDOS resumes her role as the omnipresent antagonist in Portal 2. The lark-like melody "Still Alive" at the end of Portal was evidence enough. Chell's fate, however, remained a wildcard until the aforementioned update. Previously, we saw Chell catapulted to freedom following GLaDOS' demise. Assuming she avoided any grievous injures, her escape was fathomable. Now we know better. She's back in captivity one again.
One new detail complicates Valve's carefully implemented continuity - Portal 2 takes place hundreds of years after the original game. We assume the party associate stashed Chell in some sort of stasis chamber in which she's quietly passed time.
While Chell appears relatively unscathed, the Aperture Science facilities haven't fared as well. Centuries after the explosion, no one has been around to repair sprawling campus. Overgrown areas are interspersed with cold and clinical test chambers, now in various stages of decay. As far as we (and Chell) can tell, no one has stepped foot in the derelict labs for decades. But loneliness won't overtake you, as a cast of slightly less organic characters has thrived in GLaDOS' absence. At the end of Portal, illuminated by a candle atop the tabled cake, rows upon rows of personality cores were awakened. These spheres are the same as those Chell ripped from GLaDOS' breast as she incinerated her captor one piece at a time. Introducing this new "species" allows Valve the chance to integrate unique AI personalities without introducing human peers. It also addresses the concern that returning to an isolated GLaDOS and Chell relationship would feel too much like a retread.