So What Happened? is a series I do for my website which takes the most complex game stories and breaks them down for easier digestion through narration, background information, and clips.
The story of Halo Wars was much more complex than other Halo games had been up to that point, and relied heavily on knowledge of the Halo Expanded Universe. Because of that, a lot of things were not explained in the game, and may have left players puzzled as to just what happened.
Props to the old Halo Wars Forum.