After safely escaping the collapsing ruins, the narrative goes into another cutscene in Cozumel, Mexico.
This cutscene describes Dr Dominguez who is leading a few trinity digs in the area. Lara starts describing in detail how the relics they've been searching for are not in Brazil but in Peru. Trinity had always been searching in the wrong place. Dr Dominguez is called upon by someone regarding something of his interest. As he begins to leave the area, Lara and Jonah start follow him.
You have to take control of Lara now and search for Dr. Dominguez. You need to walk up to the gate following the marker and there you will find Dr. Dominguez entering through the guarded gate. Jonah now tries to have a random conversation with the gatekeepers which keeps them distracted enough to let Lara jump through another gate nearby. Once you're inside all you need to do is walk the path until you reach an open gate from where another path continues.
After walking a bit, you will encounter some soldiers threatening to kill an archaeologist. You need to rescue the archaeologist by stealth killing the two soldiers on the spot.
Now, you will be instructed on how to highlight the objects of interest. Gathering resource containers, plants and stuff of the like is recommended as they prove to be helpful in the long run. Now, scramble up the wall and it will be followed by a cutscene depicting Ix Chel, the Goddess of the full moon and Chak Chel, the new moon.
You will be now introduced with the rope grappling features. Follow the game instructions carefully and everything will be fine.
After the climbing session, you will enter a cave where you will be taught how to use the rope pulling feature using your bow and arrows. The moment you pass through, you will be met with trap spikes enough to kill you. Just scramble through it and keep progressing further.
You will now enter a huge room with loads of stuff to collect. Once you're done collecting dive into the water at the center of the room. While underwater, be sure to keep restoring your breath using air pockets found on the way. You will be attacked by an eel after which you have to lunge up through a narrow passage with a part of which falling on you. Press the button indicated repeatedly to escape out of the water.
Keep progressing and in the next area, you will find yourself before an underground temple. Here you will find a number of platforms suspended using ropes. You need to make your way through them. In the next area, you will find a cart near an underground temple. Break the wall in front of it using your rope and push the cart down. In the next area, you the game will teach you tethering that is how to connect two tether-able points using a rope so you could climb across.
Progress further for a while and you will find the cart puzzle. Here you have to push the cart onto a rotatable track.
Rotate the cart until it's back is facing the side from which you would push. Now, attach another rope to the cart and pull it up. Cut off the rope and cart will break through the debris. Jump on the rightmost platform through an elevated point on the cliff. You need to do a bit of climbing and ledging along the next path. You will loads of interesting stuff.
An inscription that depicts the Silver Box of Ix Chel and says that the box will summon the God Kulkulkan, a series of cataclysms, a tsunami, storm and an earthquake. Lara then aligns the stars in the middle which reveals a knife which unlocks the Silver Box of Ix Chel.
Lara takes the knife which triggers an earthquake. Make your way out and you will be taught how to break through weak walls. Hide behind the vegetation on the walls and stealth kill the man there. Proceed to the next area. Here you have to go through many enemies. It is advisable to resort to stealth attacks. Keep using your special vision to detect which of the enemies are safe to be taken down in stealth. Red indicates that it's not safe and yellow indicates that it's safe.
In the next area take out four men silently and proceed. Now a helicopter appears with a bunch of men trying to attack you. Never open fire. Taking some cover is always helpful. Headshots aren't really effective at these bunch of men owing to the fact they are wearing helmets. Make use of the game's highlighting feature and keep changing your cover to keep your enemies confused. After you are done, pry open the gate and move ahead.
A cutscene starts where Lara gets captured by Dr. Dominguez who asks her for the Silver Box of Ix Chel. When Lara is unable to produce it he says that there will only be an apocalypse and the death of the Sun without the box. A tsunami starts and he says that Lara is the cause of it.
While floating in the waters you take control of Lara. All you have to now do is just dodge the obstacles in between the way. A cutscene starts after a while where Lara dives underwater. Now you have to swim your way out into the open. Be sure to make use of trapped air pockets to restore your breath.
In the next hallway swim up and you will find a wrecked van. Get inside it and break the window of its rear door. Do a bit of parkour after which you will be required to climb up a building. There you find Jonah.
A cutscene starts where Lara tell Jonah about all that happened with Dr. Dominguez and also that she wants to get to Hidden city before Trinity. Jonah convinces Lara to stay back for the while and help out the people in misery first. Now, we can proceed to the next part The Peruvian Jungle Part-1.