The Borealis is phasing in and out of reality. Rescue Dr Mossman from the Combine, she has details to make the Borealis phase in for enough time to get Freeman+Alyx+Mossman on board, chased by Combine.
While on board, discover Borealis is moving through Time as well as Space. Mossman wants Borealis recovered for the Resistance, Alyx wants it destroyed. They fight, Alyx kills Mossman.
Borealis reconfigured to fly through Space to Combine planet to try to destroy it with explosion, as they arrive G-man takes Alyx off the ship, Vortigaunts take Freeman.
Combine world too massive, powered by a Dyson sphere, Borealis explosion does nothing.
Freeman back on Earth sometime in the future, won't take part in any more conflict with Combine.