The transcript that was posted is essentially a letter from Freeman to the player detailing his story just after the events transpired.
Basically Freeman went to look for a time traveling ship or something, found it then turned it into a time traveling time bomb to attack the Combine.
Just as they were about to complete their suicide mission, GMan teleports Alyx away leaving Freeman to die. Freeman sees the Combine home world for a brief moment and sees how futile the effort is.
Vortigaunts teleport Freeman away into the future or some shit and the player is left to wonder whether the rebellion was a success or not.
If that's how they were planning on ending it, I'm almost glad it never got released >_> ---
"Life's a game. It's meant to be played." "Amateurs built the Ark. Professionals built the Titanic."