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The following deals with some of the theories about the G-Man and his allegiances.
Remember that this is a theory.
The G-Man wanted the Black Mesa incident to occur, as he was seen arguing with a scientist, possible telling him to boost the anti-mass spectrometer 105%. Since he was seen governing where the main characters when in each of the three Half-Life games, it can be theorized that Black Mesa was a sort of test for each of the three characters (Gordon Freeman, Shephard, and Calhoun), since each would be directly or indirectly carrying out the G-Man's motives later (not Shephard yet).
Again, another theory. The G-man did NOT want the Black Mesa Incident to occur. This is supported by a specific line in the Half-Life 2 script that said that the G-Man was telling the scientist back in Half-Life NOT to boost the spectrometer. Although all acknowledge that the G-Man has been more or less governing the main characters since Half-Life, these theorizers do not believe that the Black Mesa incident served the G-Man's purposes. A possible reason for the G-Man's intervention was to make sure that the portal to Xen was closed. The G-Man most likely hired Gordon because he viewed him as a valuable tool for later on.
The final theory is that the G-man is an alien life-form disguised as a human, who is part of the rebellion against the Combine that came to earth to recruit fighters against the Combine. When the G-man came to earth, he tried to stop the resonance cascade but failed. He then took notice of two people involved in the incident. The first was a theoretical physicist who survived against all odds in the Black Mesa facility & an H.E.C.U. marine (Adrian Shepard), who managed to do the same. When he deemed Gordon to be more useful than Shepard, he confined them both in a "slow teleport" (a.k.a. temporal stasis). This event also explains G-man allowing the Citadel explode in HL2E1, since he would get the Combine to earth en mass to defeat them here.
One of the original theories about the G-man was that he was the mysterious administrator of Black Mesa, judging by the Black Mesa logo on his briefcase. This was removed when Half-Life 2 was released. It is now known that Breen, the Combine Earth Administrator was the Administrator of Black Mesa during the Resonance Cascade.
The Bottom Line
Most likely, Valve did not have everything planned out at the time of Half-Life. They may have intended the G-Man to be the administrator, but then later thought it would be an interesting twist if he weren’t. However, Valve plans to release more information about the G-Man and the Combine throughout their new episodic content.