ASBusinessMagnet wrote:
That's funny. Let me give my own longish theory.
G-Man is actually the leader of the Combine, disguising himself as a respectable human being for the human beings, as a respectable Combine for the Combine and as a respectable Xen Alien for the Xen Aliens. But when he appears with the Vortigaunts, he simply transforms into a Vortigaunt (a mid-race between the Combine and the Xen), but before that he had to transform into an Overwatch (a mid-race between the Combine and the Earth) and a mysterious mixture of all three of them. But again, for humans he appears as a human.
For the briefcase part, he can even change the logo at the briefcase. At Black Mesa, the logo is Black Mesa one, but, e. g. at Microsoft, a Microsoft logo would appear. So naturally, he can show up at Aperture Science as a respectable Aperture Science employee and help Aperture Science build GLaDOS or, after 20 years, show up at Black Mesa East and help the Resistance end their portal technology (which Aperture Science did already, lol at the Resistance).
So, G-Man simply goes around transforming into every lifeform around the dimensions and helping out with technology, but the one part is missing - Gordon Freeman. I believe G-Man tries his best to show Gordon that he is not helping the Combine, but Gordon, as the games show, simply goes by himself and Alyx Vance to the Borealis. G-Man really doesn't want Gordon and Alyx there for one big reason.
[1] Because I think that in Episode Three they will discover a Combine Hideout at Earth and will be able to hide the whole explosive material in Earth to make it go BOOOOOOOOOOM!!!!!!11!!! Then, when the BOOOOOOOOOOM!!!!!!11!!! happens, Gordon and Alyx will probably hide in a base in the Moon (I can't believe that in 2023 or whatever the year Ep3 happens to be, I think it will be somewhat more like 2028-2029, there will not be a lunar base) and take the rest of the Lunar Resistance to the demolished Earth (of course if the BOOOOOOOOOOM!!!!!!11!!! doesn't make the whole Earth go BOOOOOOOOOOM!!!!!!11!!! or change its orbit) and when the Combine are no longer there, start the new life of Earth.
(go to [2])
Also, I love that phpBB has no character limit for posts. 

EDIT: I've changed my mind a little.
G-Man is not the only leader of the Combine, but GLaDOS is too, G-Man being biological and GLaDOS being technical. I first realized this when I listened to GLaDOS quote which said:
GLaDOS wrote:
We are throwing a party
Which kinda resembles:
[etouq/]Idiom pa iorph, paniajo["SODaLG"=etouq]
So I believe here GLaDOS is commanding the Combine to go and kill Chell, but it fails because the Combine are stuck at the entrance (lol to the Combine).
So it is like this;
In 1986, the Combine came to Aperture Science and said to Cave Johnson: "We've conquered your company. Select from either you or your wife, and we'll help you defeat Black Mesa." Cave Johnson selected his wife and then the Combine and Aperture Science employees built GLaDOS (1999?). When GLaDOS was on for 4 years, the Combine went to Black Mesa and caused Black Mesa Incident (2003?). After that, when both of them were taken out, the Combine used their powers to defeat Earth (Seven Hour War, 2013?)
But the Resistance managed to revenge and (go to [1])
[2] (The Final Destruction, 2028-2029?)
And so the war between the Combine and the Mankind resulted in the Mankind's victory.
Fast forward to 3001, the Combine came in to the reestablished greatness of Black Mesa, conquered them (again) and went to Aperture Science to get reestabilished GLaDOS. Then they failed, when the reincarnate of GLaDOS and me (Aperture Science Business Magnet) pwned them. Then we married (so now she is known as GL@DDA Magnet) and with Aperture Science Madmanic Inventions pwned them again. The Combine vs. the Mankind 0 : 2. 