Trent Roman wrote:
(Was that Malak at the head of the Sith Armada, or just somebody who looks like him?)
Just looks like him. Malak has been dead for about 300 years at this point. That Sith character isn't given a name.
The Jedi Temple was attacked, by over twenty Sith led by an unknown Sith, his Twi'lek aide and assisted by a bounty hunter.
Here's a video showing the timeline of the game:
And you can read the first webcomic (Threat of Peace) leading up to the game on the main site.