A few changes to the fight were made in 1.3.
1) He doesnt stealth twice
2) Cannot be interrupted
3) stab ability does far less damage

Just some TFE with a group, Enjoy

The False Emperor [Hard Mode] Flashpoint with written strategy for every boss encounter. Tregg the Destroyer, Jindo Krey, HK-47, Sith Entity and Darth Malgus. Mercenary view, healer.
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Guide to The False Emperor normal mode
Messores Republicae
Server: Sword of Ajunta Pall

Your first boss in Darth Malgus’s Space Station is Tregg the Destroyer. Three adds, which you can dps down or cc before switching to Tregg, are also a part of the pull. Tregg has two abilities: Hunter’s Leap and Whirlwind Slash. He will periodically leap to a random party member and knock them back, make sure you position yourself so that you won’t be knocked off the side of the bridge. Whirlwind slash is avoided by immediately running out of the aoe. Also, we did notice that he jumped targets much less when we had one of the adds cc’d instead of killing all of them, but we were unable to confirm this.

Shortly after Tregg you will encounter Jindo Krey, one of Malgus’s hired Bounty Hunters. Jindo has 4 abilities: an electro dart charge, which allows him to stun party members for 3 seconds, a flame sweep that does aoe damage, a grapple that pulls a single party member to him, and a warship missile barrage from his starship. Also, his starship will fire missiles at random party members throughout the fight. The missile damage boosts up periodically and caps out at 400% of its original damage. In order to stop this, have a dps focus on using the turrets to take down the ship. | One turret shot will take down the starship, but it must be the turret directly in front of it. While the ship is away, blue circles will appear on the ground showing where rockets will attack. Be sure to stay out of them. When the ship comes back it will always start in front of the middle turret. Make sure to have your party interrupt Jindo’s stun and grapple while the dps is trying to down the starship. After five times, the ship will be down for good and you can just worry about dpsing Jindo. Jindo’s last ability is a shield he casts on himself that allows him to take no damage. When the barrier bursts however, Jindo takes all of the damage done to the shield instantly.

Your next fight will be against Prototype droids b16 and a14. This fight is a simple tank and spank with only two abilities: one droid will go invulnerable while the other is able to be dpsed. They switch states throughout the fight. The invulnerable droid will throw a debuff on random party members that makes them take 10% more damage. The blue circle underneath the invulnerable droid is supposed to add a buff to the vulnerable one, but at the time of this video this effect was not applicable.

You’ve seen him in action, you’ve fought beside him in KotOR 1 and 2, the next boss is none other than the big droid himself: HK-47. HKs moves cannot be interrupted. You’re going to have to grit through them. Burst, however, can be avoided by your tank facing HK away from the party because it is has a cone of aoe damage. Once HK is brought below 40% he will cast stealth on himself. He will enter stealth, then appear next to his target. After the target is stunned, HK enters stealth a second time. This time he starts casting stab, which will one shot even your tank. You stop this by casting aoes next to the stunned party member as soon as possible. This will happen periodically throughout the fight until he is killed.

If you’ve done the bonuses you’ll be able to take a short detour and fight the Sith Entity. The Sith Entity has an aoe knockback, so keep your ranged away from him. He will also split into three mobs a few times during the fight. Take down the casters first and make sure you interrupt their heals.

Now the final boss awaits you in his throne room: Darth Malgus. The fight has two phases. In the first phase Malgus has a single target pushback. Your group should position themselves between malgus and a wall so that they can quickly get back up. Malgus also has an unavoidable aoe dps. During the fight Malgus will instill doubt in one of your party members. All other party members will be force choked. This does no damage, but is a very long stun. During this time the selected party member will have to fight Malgus alone. Malgus will use Vengeful Strikes. This does a decent amount of damage and should be interrupted. | The second phase starts when Malgus is at nine percent hp if he has already instilled doubt in all four party members. If your dps is fast enough, you can kill him before he puts doubt in the fourth party member. Once he’s entered his second phase he can only be killed by pushing him off the edge of the bridge at the front of his throne room. Your tank should kite him as close to the ledge as possible once Malgus reaches 15% hp because malgus will be extremely difficult to kite in the second phase. At this time Malgus will be constantly casting force lightning. You will need to cast two knockbacks within the same lightning cast in order to knock him over the ledge.