Ok, I've done a lot of reading and research, and this is how I put together the plot. Heavy spoilers, obviously.
Let's start with the G-man. The G-man is, I think, a good guy overall. At the same time, he's mercenary. He works as a contracter, selling the services of Gordon Freeman to the highest bidder. Evidence - he tells you as much at the end of HL2.
Now, look at Freemans name. Free Man. He goes around Freeing people. In HL1, look at the vortigaunts. They have shackles around their arms - they're slaves. In HL1, Freeman is freeing them.
Obviously, this is set up by the G-man. The G-man, therefore, must have gotten the sample to the Anamolous Materials lab. This sample is special, the scientists tell you as much. When used, it makes the Border world Xen and Earth unite, and Xen creatures appear here. This was intended by the G-man so that Gordon would do what he had to. In the level in HL1 "Questionable Ethics", we see caged Border World creatures. Because the scientists are either elsewhere or dead, and the setups are complex, we must assume the creatures have been there for a while, and so the humans have been visiting the Border world a number of times.
Now, at the end of HL1, we see the boss, who seems to be ruling Xen. By killing him, you free the vortigaunts. However, the shackles on his wrists indicate that he was coerced into ruling Xen - presumably by the combine. So, the combine take an interest in Earth. Freeman is told he has a job, and steps through a teleport.
In HL1 and 2, there are no cutscenes, no one week later or anything - it happens directly through Freeman's eyes. Yet he appears years later in City 17. We must assume then, that to Freeman no time has passed. In HL2, there is a slow teleport that takes a week. The G-mans teleport, then, must have been a slow teleport of ten years.
So Freeman is in City 17, being hired by the rebels to free them. We see the G-man negotiating with the rebels through a telescope at one stage. We also here how Alyx says he saved her even though he wasn't obligated to, and Breen says he could hire Freeman. Freeman is working for the G-man.
The Combine Benfactors are never seen, but the Combine troops are. They are the army dudes, and are part human part combine. Presumably, they were only recently created, as Breen says that their failure won't allow them to prove themselves an indispensable part of the Combine millitary.
The gunships and striders, BTW, are Combine weapons. Not Xen, the Xen are a people opressed by the Combine. Also, the Civil patrol are not Combine, but Human. Note how easily they go down, and how Barney managed to infiltrate a suit. They're clearly designed for Humans.
The final clue is the G-man at the end talking about time. Evidently, destroying the machine as it opened a portal to the Combine homeworld created some kind of Timewarp on the same principles as the Slow teleport. What happens now is something left unknown until HL3.
Oh, and Breen is trying to deal with the Combine, and let them take some control of Earth as they did Xen, as opposed to fighting them, as the rebels would.
