Thank you schall you just gave me an idea...If it began in the hangar it would have to have a sort of (in the last episode) moment...Where it viewed all the big memories of EP2 and then finally showing Eli vance's death (purposely) I reckon if it is like that it will mostly show all information...
My guess is that the Aperature science ship is the Borealis. And you have to destroy the ship because it perhaps holds the weapon to the combine portal?
The combine advisor Is easy to kill, just as long as it doesn't have the ability to lift up and throw objects against there will...I will...