The music in the Ancient cutscene after that really conveys their despair. "...We know we will soon be gone, and we can see our fate as others will see it. There will be little legacy, no great expressions of what we once were..."
The Destruction of the GTD Galatea, and with it, Admiral Wolf. Sure, he spent most of the game as a disembodied voice, but it was really sad to see him go down with the ship.