I agree with AustinQ's contribution. That is very likely and well thought-out. My idea is this:
HL3: Gordon and Alyx go into the Borealis, and discover plans for both the Portal gun and time travel. They slowly discover that the Borealis has been transported through time and crashed into the iceberg, and that it could be transported through time again.
P3: GLaDOS kicks Chell out of the facility, and finally gets back to rebuilding the facility without any interruptions. She discovers that the original Portal gun was left on the moon, so she builds another 2 for Atlas & P-Body. She finds out about the time travel experiments in earlier stages of Aperture Science, and she finds out the the Borealis is still stuck in the HL3 timeline. She activates the time travel again and sends the Borealis into the Portal timeline, along with Gordon & Alyx.
HL3: Gordon and Alyx are transported into Aperture Science, and GLaDOS starts using them for testing, as they have a gravity gun. GLaDOS gives them the two Portal guns for them to do gravity gun based co-operative testing. Gordon uses a combination of his crowbar, gravity gun, and portal gun to escape, taking one of the portal guns with him, but dropping his gravity gun, and second portal gun. He gets his scientists to rebuild the gravity gun, and battles the combine again with his previous arsenal as well as the portal gun.
P3: Chell starts to walk away from the facility and sees Alyx and Gordon escaping. She picks up the portal gun and gravity gun, and enters the facility again to find her parents, likely to be Cave and Caroline (as AustinQ pointed out). She has to battle her way through the new gravity gun based tests to get back into the main Aperture Science building. GLaDOS sees her with the Portal gun and changes the tests to try and make her give up the Portal gun, as GLaDOS wants her out. Chell ends up escaping and finding her parents, Cave and Caroline, and GLaDOS sets them free to live a happy life. They live in City 17, and Gordon & Chell just pass each other by in the town.
P3: GLaDOS kicks Chell out of the facility, and finally gets back to rebuilding the facility without any interruptions. She discovers that the original Portal gun was left on the moon, so she builds another 2 for Atlas & P-Body. She finds out about the time travel experiments in earlier stages of Aperture Science, and she finds out the the Borealis is still stuck in the HL3 timeline. She activates the time travel again and sends the Borealis into the Portal timeline, along with Gordon & Alyx.
HL3: Gordon and Alyx are transported into Aperture Science, and GLaDOS starts using them for testing, as they have a gravity gun. GLaDOS gives them the two Portal guns for them to do gravity gun based co-operative testing. Gordon uses a combination of his crowbar, gravity gun, and portal gun to escape, taking one of the portal guns with him, but dropping his gravity gun, and second portal gun. He gets his scientists to rebuild the gravity gun, and battles the combine again with his previous arsenal as well as the portal gun.
P3: Chell starts to walk away from the facility and sees Alyx and Gordon escaping. She picks up the portal gun and gravity gun, and enters the facility again to find her parents, likely to be Cave and Caroline (as AustinQ pointed out). She has to battle her way through the new gravity gun based tests to get back into the main Aperture Science building. GLaDOS sees her with the Portal gun and changes the tests to try and make her give up the Portal gun, as GLaDOS wants her out. Chell ends up escaping and finding her parents, Cave and Caroline, and GLaDOS sets them free to live a happy life. They live in City 17, and Gordon & Chell just pass each other by in the town.
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