Drake, Elena, and Chloe have escaped Lazarevic's grasp and must now find the Cintamani Stone before he does. Nate and Elena take off their coats and Chloe grabs a gun off of the dead bodies and gives it to Elena.
Chloe then suggests they head back to the entrance now that Lazarevic and his army are in the city. However, Nate and Elena disagree with her, saying they need to go after the Cintamani Stone and destroy it to prevent Lazarevic from getting a hold of it. Chloe believes that Lazarevic is just fulfilling some prophecy that the stone will make him invincible. Nate reminds her of how strong the guardians were and says that something strange is going on in Shambhala. Chloe uses that as another reason to leave while they still have a chance. Nate then reminds her that she is the one who said that he should take Lazarevic down, but she says it will not end that way, but end with them getting killed. They try to convince her to take their side. She thinks they are crazy for making this decision, but she reluctantly agrees.
They press on the temple, fighting several guardians and Lazarevic's men along the way. As they finally reach the temple, they end up in a large room with Lazarevic's men fighting the Guardians. The three must intervene in order to clear the room so they can press on. Once done, they make their way upstairs to the stone. Chloe picks up a blunt object and insists on smashing the stone so they can leave, but Nate halts her and notices something odd about the stone. He examines the stone closely and realizes that Marco Polo was wrong all along. It is not actually a stone, but the tree sap from the Tree of Life. They look down at the tree and spot Lazarevic heading towards it. Nate then remembers the black teeth from the Guardians and the bodies in Borneo. He realizes that they ate the resin and it somehow changed them. Flynn shows up behind them, mortally wounded from being brutally beaten by Lazarevic, who found no use for him. He states that Zoran was more clever than he looks. Elena expresses a certain degree of sympathy for the wounded Flynn and says they can help him. However, Flynn states that it is not that simple. Before Nate tries to reason with him, he pulls out a live grenade and drops it onto the ground. It blows up, killing him and seriously wounding Elene. Nate and Chloe help her up and they walk her out of the room. They then encounter more of Lazarevic's men. While Chloe holds onto Elena, Nate clears the way by taking out all of the goons.
Once they make it past the goons, they set Elena down. Nate tells Chloe to take and Elena and head for the gate as quickly as possible. Nate heads down to the tree to confront Lazarevic.
You start out running from Lazarevic's men and the guardians. Run through the ruins and try to dodge incoming fire. You will come to a platform so jump onto it. A cutscene will show an RPG soldier getting tackled by a Guardian. At the same time, he will fire his weapon and break the brace that is holding the platform in place. It will start sliding down a path and you then regain control of Nate.
Stay away from Dragan, who has jumped onto the platform. The platform will eventually crash and another cutscene will show him speared on a tree branch. Jump off into a small courtyard and find AK 47s, 92FS-9mms, and grenades. There is a treasure on one of the statues that you climb across, shoot it and it will fall. Two Guardians will appear armed withcrossbows. Shoot at them constantly. A good, if risky, idea is to make them charge at you and unload bullets into them. Try to stay on the run. Eventually, one will die so take his crossbow. On Crushing, it can take 3-4 shots to kill one. Be ready to kill a third one that throws resin explosives. After finishing them all off, go to the alcove and climb up to the top. Jump to the vine and continue until you reach the area where the Guardians came from. Use the sap to make your way through the obstacles, but make sure to stand clear of the explosion. When you get inside, jump from the pole to the wall and jump back into the room. Shoot the sap and move through until you reach a large courtyard. Go to the end of the courtyard and you will find a door with a broken weight. Before you can do anything, about a dozen soldiers appear. One sniper, one RPG trooper and one heavy weapons trooper. They will also have a few other relatively normal soldiers. I recommend stealthing the two guards who are patrolling near the giant, fallen pillar. Do your best to try and surprise the more difficult soldiers with heavy firepower, especially the one with the GAU. After you have done that, two Guardians will appear. Kill them and open the gate. I recommend you don't try to use the mini gun against them because they can just kill you quickly with their crossbows. After going through the gate, drop off the ledge and three soldiers will be walking away from you. Do not try to stealth kill any of them. Instead, look to the top right and you will see a specialist with a grenade launcher. Kill him first, then there will be about 3 heavies with SAS shotguns, the 3 normal soldiers, and a sniper. After you kill them, 2 more heavies and a specialist come including another sniper. Kill them, climb the wall they came from, and drop down the hole. One heavy and 3 soldiers will appear. There are two options to killing them. You can kill them normally, or shoot the sap near them when they first appear. This will kill them all instantly. Push the wagon to get up a ledge, you will then be at the temple stairs. A treasure is right there when you climb up, so look behind you. Go up the huge stairs then, find the soldiers and Guardians fighting inside. There will be one heavy trooper and a couple of skull heavies, some shotgunners, and other troops.There are about 6 or 7 guardians, 2 of them throw the explosive resin, the others are archers. Its better to sit back and watch them kill each other off, the guardians win most of the time. When the first 3 die, 4 more come, 2 archers and 2 resin bomb throwers. After you kill them all, make your way up the stairs the guardians come from and then you will reach the end of the level.