The medical facility in the eastern corner here holds a dying Selkath who'll give you a personal token that you'll need shortly. Once you have it, head to the dormitory to the west and speak to the Selkath inside. There is a variety of possible outcomes to this encounter, the most favorable of which involves showing the token to the Selkath you speak to, and then using persuade to convince them to leave the embassy for a Light side shift. You can also use Force persuade to get them out of the complex, but this won't get you any closer to that Light side mastery you might want. Of course, you could just slaughter them all for a Dark side shift, but for reasons yet to be revealed, it's best if they leave the facility alive, even if you are a Dark Jedi.
After that conversation (or battle), head through the training room to the east. You might want to save your game first. Just a suggestion.
The Dark Jedi Master here is another toughie, but not impossible. He'll have two Selkath groupies who attack with blasters, but ignore them for the moment. The key here is to incapacitate the Jedi before he can do serious damage; both whirlwind and stasis seem to have a decent chance of connecting, though he will resist your powers more often then not. Once he's incapacitated, gang up on him and take him down hard. Leave the Selkath alone until after he's dead; they're not going to be hurting your Jedi that much anyway.
Make sure you use cure or heal after your party gets hit with Force lightning.
After the Jedi falls, search his body, and then rifle through the footlocker in the next room. Luckily for you, the Jedi kept detailed financial records of Malak's empire--you'll use this information to take him to court for tax evasion later on. Yeah, he's high and mighty now, but we'll see how a few years in Alcatraz change him.
Now that you've found everything there is to find in the Sith base, proceed back to the elevator and ride up. You will encounter a group of guards seemingly intent on bringing you to trial for causing such a ruckus.
Since you managed to find the Dark Jedi Master's datapad, you'll not have to worry too much about your indiscretions. Just point it out to your arbiter, or choose to represent yourself, and then bring it to the attention of the judges. You get off on a technicality; congratulations. If you had let the Selkath represent you, you would've been executed. Head back to Roland Wann at the Republic Embassy. He'll spin you a tale about an underwater facility that the Republic has built, and you can guess where you'll head off to next.