Image source: http://orange.half-life2.com
I think many are waiting for Half-Life 2: Episode 3 to see how it all ends.
What is the long lost research vessel Borealis that Mossman discovered in the arctic ice, what secrets does it hide about how aliens could open portals to our world, and has it something to do with advanced Aperture Science?
I believe that Episode 3 will have something to do with the game Portal, wich the maker of the Half-Life games Valve released as a part of The Orange Box.
I think that it is a way to introduce the concept of portals so that players can familiar themselves with it, before it is being used as a part of the new gameplay in Episode 3. In the same way the Zero-Point Field Manipulator was used in Episode 1 and the Magnusson device plus the Hotrod vehicle in Episode 2.
I am very excited of what will happen in the storyline with Alyx Vance and Gordon Freeman, after one Advisor extracted all Eli Vance knows and killing him as the result.
Before being killed, he was warned by the Gman as he relayed a message through Alyx when she was being brought back to life by the Vortigaunts. He got the same message just before all went wrong in Half-Life 1 at the Black Mesa facility.
"Prepare for unforeseen consequences"
"Unforeseen Consquences" were also the second chapter after the portal to Xen was opened.
Questions I am looking foreward to get some more answers on in Episode 3 is:
Who is Gman really? What is he after? And what will he be in the end?
There is one theory that he employed and is helping Gordon because he has seen the future, and does not like the people of earth being enslaved by the Combines. And that he is working for "some kind of" or the goverment and that Gman just means Goverment Man.
He puts Gordon Freeman in and out of a "stasis" in time when he needs him for an assignment. But he is brought out of that stasis in Episode 1 with the help of the Vortigounts and their distracting of Gman.
The Vortigaunts was one of Freemans main enemy in Half-Life 1 because Nihilith, the mind enslaving leader of Xen, controlled them. There is also something not answered about them I think and their connection to Gman. There is also something more to be revealed about the scientists from Black Mesa: Dr. Magnusson, Kleiner, Eli and Mossman.
In Episode 2 it was revealed that Gman saved the main heroine and Gordon Freemans companion Alyx for "his own purposes" back at the Black Mesa facility.
There is also clearly something more than just friendship between Alyx and Gordon, which maybe will evolve even more in Episode 3.
A recent interview with one of Valve's main guy Doug Lombardi by StuffWeLike.com opens however for that the story does not end with Episode 3:
"TS-SWL: Are there any current plans after Episode 3 to have a Half Life 3?
DL: We haven’t announced anything specific, but Half-Life won’t end at Episode Three – hang on to your crowbars!"
I definitely like that answer because I am a big fan of the games, but at the same time it would be great to see a exciting end after 10-11 years since Half-Life 1 first was released :)
Sources: Wikipedia, and from playing the games.