Chell didn't know how it happened, but all of a sudden she was in a hallway, away from her bedroom. She didn't remember traveling here, but that's not what mattered. What mattered was that she couldn't feel or move her legs. She tried vehemently, attempting to force those neurons in her legs to cooperate, but there was nothing.

Then there were her arms. Gone. Unusable. No feeling there either. What she could feel was her face and torso, but they were different. Her proprioception told her that they now had a completely different shape, and... breathing. She wasn't breathing. She was still alive, could still probably talk if she had the desire to, but there was nothing. No smell, no taste, only sight and sound.

And she tried in vain to move, trying to feel where her arms and legs had gone until she realized that she had moved forward somehow. And she felt it too, something on her back that was enabling her to move, so she tried again, finding she could indeed travel on a fixed path.

Fixed path. She looked up. It was a rail.

...

It couldn't be. This was another nightmare, wasn't it? But as she glanced at a blurry reflection on a sheet of metal, she saw what she had become. Instead of screaming, she merely froze there once more, unable to even process this.

((tl;dr: Chell and Wheatley have swapped bodies.))