My theories on the Ep3 storyline:
After the death of Eli, Alyx and Gordon escape from combine forces closing in and go into hiding in the arctic.
The combine sends eyebots all over the world and eventally finds them.
In the meantime, Gordon is almost killed by an enormous Bullsquid living in a frozen cave.
Then Alyx and Gordon escape the combine yet again, but they each go separate ways.
Alyx and Barney travel to a city where Kleiner is in charge and are greeted warmly.
Only Kleiner has betrayed them to the combine and both Barney and Alyx are captured.
Barney is placed in suspended animation and is sent to the new citidel being built.
So Gordon had gone to a hidden university where one of his college professors coaches him in âthe wayâ and Gordon learns some special mediation and martial arts techniques.
Gordon also learns that Alyx is his sister.
He suddenly receives an encoded radio message that Alyx and Barney are in trouble and so he rushes to rescue them.
When he gets to Kleinerâs city, he finds out that it was a trap and Alxy and Barney were the bait.
There is a long duel between the G-Man and Gordon at the end of which, his only remaining weapon, Gordonâs crowbar, is knocked out of Gordonâs hand and falls down a long ventilation shaft.
Then G-Man reveals that he is actually Gordonâs father and Gordon then screams âNoooooooo!â and jumps down the ventilation shaft after his crowbar.
He somehow survives the fall and shortly after, Alyx, Kleiner (who pulls a Mossman and switches sides again) and Dog manage to rescue him.
Stay tuned for the exciting conclusion in Episode 4 where Gordon rescues Barney and then teddy-bear creatures from Xen help Barney, Alyx, Kleiner and Dog to destroy the partly-assembled citadel while Gordon faces off with G-Man who still claims to be Gordonâs father.
WHAT?? No! I didnât rip this off from Star Wars!
(My real theories: https://sparcman.blogspot.com/2008/07/half-life-2-episode-3-speculationep-2.html)