Exit the temple by taking the path on the left corner of the room. Dive into the water and follow the objective marker to escape the flooded ruins. Stay away from the predator fishes (Piranhas) or hide into the under-water plantations to avoid their attention.

After getting out of the flooded ruins, move forward and jump on the tree. You’ll learn “Eagle’s Talon” skill here. Take out the two guards. Move forward and a cut-scene and you’ll watch a mysterious creature killing a Trinity guard.  Move forward into the next area patrolled by eight guards. Take them out and continue forward. After a short while you’ll come across a bunch of dead Trinity soldiers. Keep moving towards the objective marker to reach the ruins of Kuwaq Yaku. After entering the ruins, take the stairs on your left & head down to the basement to meet Jonah.