Objectives: Defeat Darth Malak
Don't kid yourself: no matter how virtuous you are, you won't be able to turn Malak to the Light side. It'd make for a fairly anticlimactic ending. Prepare yourself for battle with everything that you have: equip any verpine prototype shields you have, and use any and all stims in your possession, starting with an Echani battle stim, if you have one, and working your way down the ladder when that runs out.
You will not believe Malak's statistics; this is a fact. To begin with, his base attack bonus is +20, to which he adds +3 from master dueling, +1 from lightsaber focus, and his Strength mod of +9 (holy mackerel!). He will also often have an effect bonus of +5 to attack, for a total of +38 to attack. Darth Malak will whiff on an attack a whopping 5% of the time, when he rolls a natural one on his die roll; otherwise, he will hit you every time he swings.
Someone at BioWare is a Zatoichi fan: Malak uses underhanded blocks in battle.
Every time Malak hits you, he gets an automatic +14 to damage. Ouch. He will also use every melee active combat feat at master rank, including critical strike, so it's not uncommon for him to dish out 50 damage or more on a critical hit. Note that, even on regular hits, he will usually do enough damage to take him over the limit of your energy shield, so that you will take at least a bit of damage from every shot.
When it comes to protection, Malak is quite understandably the hardest enemy to hit in the entire game, with a ranking of 37 defense through some inscrutable series of bonuses. With any luck, your attack bonus will be around +27, making it a simple fifty-fifty chance to hit. If you're at any less, though, you'll need to do whatever it takes to boost your attack rating, such as switching from a dual lightsaber to a single-handed one. If you can't hit your opponent, you won't have much of a chance to win the fight.
As expected, Malak keeps himself sheathed in Force immunity for most of the battle, making it difficult for any of your offensive Force powers to connect, but even if he was defenseless, his massive saving throw bonuses would still protect him from most of what you could do. It's best to focus on settling the conflict with your lightsaber. If you can combine master speed with master flurry, or even just use master speed by itself, you should be able to get at least one successful hit in on Malak per turn, assuming you haven't completely neglected your attack bonus. Master speed will be critical to this fight, so try to reserve your Force points by any means necessary. Life support packs can be used in place of heal, for instance, assuming you have a decent treat injury score.
You'll need to use a Force Power to mercy-kill these Jedi before Malak can heal himself.
The catch to this battle is that Malak can completely regenerate himself every once in a while, by smashing open one of the creepy floating Jedi that dot the area. After you knock him down to about half of his vitality, he'll take a moment to explain who the Jedi are (and, since conversations take place in real-time, your battle stims, Force powers, and energy shields will have their clocks ticking all the while), and then heal himself completely. In order to prevent this from happening, you'll need to run around the level, destroying the trapped Jedi with your Force powers. Make sure you have Speed activated, then destroy all of the Jedi capsules in one run, if possible, while avoiding Malak as best you can. Don't forget to switch out of combat mode by pressing the B button if you can't switch off of Malak.