The Reaper Heart / Brain Room
This room features the remnants of the human Reaper from Mass Effect 2. What's actually left in the room depends on a decision you made in Mass Effect 2:
-If you imported a save with the Collector Base destroyed, or you started a new game in Mass Effect 3, the Reaper heart will appear in this room.
-If you imported a save with the Collector Base salvaged, the Reaper brain will appear here.
Head forward down the catwalk to trigger the next fight. A Phantom appears close to you while reinforcements arrive further down the catwalk. The reinforcements consist of Assault Troopers, more Phantoms, and a Nemesis. Run forward and take down the first Phantom quickly, then get into cover before the Nemesis starts sniping you. When you're clear, proceed down the catwalk and up the ladder. On the next level, pick up some ammo, then continue your climb. Different level, same group of enemies. Before you go through the door, at the top of the final ladder, head down the catwalk away from the door to find a Med Kit and some ammo.
Go back to the door and head through. Halfway through the next room, there is another Med Kit and some more ammo on the floor on your left. There's also a Video Console you can activate to learn more about Cerberus troops and the Illusive Man, and some back story on Paul Grayson from the Mass Effect Books. Go through the door on the far side of the room, then up the ramp and through the door at the top.
Boss Fight: Kai Leng
The Kai Leng fight is broken up into several waves. At the very start of the first wave, Leng will grapple with you, and you'll need to mash the melee attack button rapidly to throw him off. Immediately have EDI and anyone else with Overload use it on Leng. Hit him a few more times and his Shields will lock and you can do no more damage. He'll kneel down and summon Troopers. It may seem like you should enter the pit area opposite the Troopers, but if you keep moving around the perimeter of the room you have a better angle to take them out.
Use EDI's decoy and send your squad to opposite sides of the room to spread out the enemy fire. In this wave, you can reduce Leng's Shields to one bar. Keep using overload and hit him with Disruptor Ammo whenever you can. The Sniper Rifle Concentration Mod is a great asset here since you can slow time and nail him. You can also use melee attacks if your character is built for it. Leng's deadliest attack is a wave of energy that completely drops your shields. You can dodge this or take cover from it, but if you get hit, get ready to use a Med Kit.
When Leng goes down on one knee again he'll barely recover, but more Troopers will arrive. It's the third wave of enemies that's a problem: Phantoms are tough to deal with in the trenches, so be sure to head for the sides of the room. They are close-range enemies, so give them some distance between you and your squad. Hopefully you can continue to nail Leng from the sidelines. Once his shield is gone, use your weapons to whittle away his health bar. One solid shot to the head from a Sniper Rifle can do wonders.
Finally, Leng will fall. In the next cut scene, prepare for a Renegade Interrupt moment to put him down for good and score some points. Avoid this if you are playing 100% Paragon. Finally, you will have a chance at a Paragon/Renegade Interrupt with the Prothean hologram at the end.