Here are precise directions for one method of defeating Malak. This method assumes you are playing Light Side. Most of the advice below can be found in various posts throughout this site, but if you are struggling with this battle and would appreciate a very detailed, step-by-step walkthrough, here it is.
First, general principles:
1) Never engage Malak in hand-to-hand combat. Even with a lightsaber equipped with the Heart of the Guardian or the Mantle of the Force, he'll do as much damage to you as you do to him, or at least enough to make you have to stop and heal frequently, which of course just leaves you open to more attacks.
2) Don't bother trying any Force attacks on him other than Force Wave and Lightsaber Throw. Anything but these two rarely works. Use Force Wave only when you find Malak is right up in your face, and you need to put some distance between the two of you quickly. He won't be dazed, though, so run from him as soon as you have knocked him back.
3) ALWAYS keep yourself pumped with Hyper Alacrity Stims. As soon as you slow down, immediately pause and use another, then start running again.
4) Use the pause button OFTEN! Pause, look around, see where Malak is, think about where you want to go next, or initiate a stim or a saber throw, and then un-pause. If you try to do all the below without frequent pauses, you will never know for sure where Malak is, and you'll become a nervous wreck. In this battle, "Pause" is your best friend.
5) If your health is low and you find yourself nose-to-nose with Malak, don't try to heal yourself immediately. Use Force Wave (if you have it--and you really should), run to a safe distance, THEN heal.
6) Save often DURING the battle, using a new slot each time. If you get stuck and Malak kills you, you can go back to a slot that is "safe."
When you take elevator from the Command Center to the Viewing Platform, you will find yourself in front of a door. Don't pump up/shield up yet, because if you do, your shield and stims will have evaporated by the time your battle with Malak begins. Open the door. You'll see Malak ahead, at the end of a fairly long path. Nothing will begin until you reach the end of that path and step off it, so don't worry yet.
Step forward on the path about 4 meters (two "blocks") or so, and then start laying your deadliest mines. (You want to leave the first few meters of the path mine-free, so you will have some place to stand and avoid the flack when Malak eventually sets them off.)
Lay these out in a string until you get to the end of the path.
Before you exit the path, SAVE THE GAME TO A NEW SLOT! Now turn on your shield.
Quickly take a Hyper-Adrenal Stamina and a Hyper-Adrenal Alacrity in succession, and immediately step forward towards Malak.
Once Malak says, "and the victor will decide the fate of the galaxy!" battle will commence, and your screen will be paused.
Malak's first move is to turn on his own shield.
Before un-pausing, hit "Force Wave" (assuming you have that ability), then turn right and run for the right-hand ramp.
You will spend most of your time running around the viewing platform, putting and keeping distance between you and Malak.
Even with this strategy, you are going to take some damage, so pause when you must to use Life-Support Packs or Advanced Med Packs. Just don't try this when Malak is too close, or he'll just attack you right away and you'll lose any health you may have regained from the packs.
Once you have gained a comfortable distance (which shouldn't be difficult if you keep yourself pumped with Hyper-Adrenal Alacrity), hit him with a couple of Advanced Lightsaber Throws. Run again, gain some distance, and repeat. If he catches up with you before you can get in a second throw, disengage and run again. Repeat this until Malak's health is down to about 40%, at which point battle with stop and he will run to the nearest unconscious Jedi.
After you've endured his lecture on how stupid you are, he will sap the Force from the victim and revive himself to full health, and battle will commence again.
No matter where you were when this scene began, you will be moved fairly close to Malak. As you did the first time battle began, use Force Wave and run away.
Now your run-and-attack strategy changes somewhat, because you will not be attacking Malak at all. You will instead be hitting the seven remaining unconscious Jedi with Advanced Saber Throws (or some other damaging Force attack--even Destroy Droid works). Just keep running around the Viewing Platform until you are a comfortable distance from Malak, then pick a Jedi and attack.
You can attack the neighboring Jedi, too, if Malak is still far enough away. If he's too close, break off and run again. Don't even think of attacking Malak again until all seven Jedi have been "euthanized," because he will just use another Jedi to revive himself to full health.
Once you have sent the Jedi on to become one with the Force, return to your run-and-attack strategy, relying mostly on Advanced Lightsaber Throws. If you're lucky and can catch him when he has stopped to prepare an attack on you, you can throw a Thermal Detonator. If you succeed with one, just keep throwing them! The ideal situation for this is when you are on the upper terrace, and he is below, right between two ramps. If you see him stop in just those circumstances, give it a try. If he starts running again before your grenade explodes, just forget and start running again. Once you get him with a Thermal Detonator, though, he's basically helpless, as long as you keep throwing them without pause. If you have enough (I had about 30 when I entered the Viewing Platform), you can kill him this way, without using all those mines you set at the beginning.
If you don't get lucky with the grenade strategy, don't worry about it. You still have all those mines! When you've reduced his health to less than 50%, now you can make that last, glorious run down the path to the elevator door.
Malak will of course follow you (although in fits and starts--he actually stops once in a while, rather than charging all at once), and basically kill himself for you.
Chances are good, though, that before he is taken out, he will do that thing where he jumps some twenty meters through the air and lands right at your side.
Don't panic! Yes, he managed to leap over a bunch of undetonated mines, but he is not safe. Just run past him and start running down the path again. Every time I have done this, he has not gotten more than a few steps back up the path before collapsing. If you run back up the path, and Malak somehow manages to survive after detonating all those mines…well, I can only assume that your mines were not powerful enough. In that case, you'll just have to go back to the run-and-attack strategy, wearing him down with saber throws, or trying again with the Thermal Detonators.
When he finally collapses, you'll have your last dialogue with him, and then it's all auto-pilot from there.
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