What have i done?????

No, really, i completed half life two about a week befo........after it came out and ever since then i've stuggled to grasp what old Gordon Freeman has actually done. Can somone explain the story to me? Why are some of the aliens on your side now? Why do aliens come out of the capsuals? Is earth being invaded? By the looks of it Gordon knew what he was doing, I think it was just me that was confused. I understand the story takes place after Gordon manages to ecape Black Mesa and gets captured by "the man". Its an awesome game like, its just the storys a bit confusing (I'm not the best at understanding these things as Murdo knows :p ).

BTW, has anyone played punisher yet? Theres a nice referance to HL in one of the ingame cut scenes towards the end of the game.