I do apologize if i did not elaborate on what i said before, but what i originally meant was that the unprecedented complexity of the plot will most probably have you doing something totally mind blowing.

I have this theory that there will be alternate endings at the end of
episode 3, very similar to the first half-life game in that your decision will not really have any effect on the direction game plot wise.

First of all i have respect for Valve therefore i do not think they are a bunch of dip shits who would throw a gun that could allow one to manipulate 3d space into a game that is renowned for its physical obstacles (meaning there will be no portal gun). How ever that does not mean there will be no portal device!

Secondly i believe that the borialis does house portal technology capable of allowing the combine to launch a second invasion like that of the 7 hour war.

If you put together the pieces these are all reasons to justify why Eli’s dying request was to destroy the borialis. But what about the combine? Sure if we blew up the borialis the earth would be spared of the combine oppression for all eternity, but what of all the other civilizations that the combine has enslaved and will enslave? Will the people of earth just live on happily knowing that the combine are still menacing the membrane of space. No it wont; Gorden Freeman and possibly Alyx will use the portal technology to launch a well engineered insurgency on the combine empire (possibly the combine overworld).

Option 1: Choose peace for earth but not everyone else by dispatching the ship and its technology.

Option 2: Take on the entire combine empire and free the enslaved whilst putting humanity at risk.

Half Life 3 will assume that you picked option 2…