Please note that this is based off of Game Theory's theory that the companion cubes are actually people stuffed in boxes, just a little FYI. Enjoy!
It was a late night at Aperture Science, when GLaDOS was trying to make some new turrets that would react with companion cubes. Suddenly she detected an intelligence sphere sized object hurtling towards the facility. GLaDOS thought to herself Oh my God that moron figured a way to get out of space didn't he!? Then Wheatly came tumbling in.
He immediately gloated that he managed to get back, which was an obvious mistake. GLaDOS then dropped him in the incinerator. Wheatly stayed down there for nearly a month before GLaDOS dragged him out, surprised he wasn't dead.
GLaDOS then stated "You know, you're so idiotic you might just be what I need, to test out some new… obstacles I've created.
Wheatly quickly responded "HOW ARE YOU GOING TO HAVE ME BLOODY TEST, IM A CORE!" Wheatly thought to himself this is it, this is IT. She's gone mad!
GLaDOS let out a homicidal laugh "All I am going to say is that it will be VERY painful."
A Day Later
GLaDOS had put Wheatly into sleep mode and into a human-robot thingy, CYBORG! CYBORG! He's a Cyborg. Nonetheless a lame one, but whatever. When Wheatly awoke he had a panic attack thinking he truly was a human.
GLaDOS interrupted his panic by stating "I see you like your new body, I made it myself. Oh, yeah and you ARE going to help me with the new obstacles. Happy testing…. Moron."