There is a lever near your entry position that opens the doors ahead. Follow the Nali priest outside to a Stinger and a series of levers that will eventually open the doors ahead of you. Enter the arch on your left, kill the Krall that attack, and enter the next arches. There is a dead soldier and an AutoMag near the cliff edge, and a pen of calves in the back. Keep going around the outside, kill the Skaarj and get the Razorblades from the barrels near the crucified Nali.
Turn back, and enter the graveyard. A stone monument will push aside and the button beneath it will reveal a lift in the grave ahead. Ride it down to find a Flak Cannon and Shells, keep going down to reach the tombs and search them for equipment. Swim through the well and surface. Two Krall are waiting in the courtyard.
From the well above the tombs, walk left to the wooden landing over the cliff edge. Jump to the ledge below and follow it to your right. The first passage on your right leads to some barrels containing AutoMags. Keep following the passage, attack the Krall on the landing to your left. Take the stairs down to the room below, and shoot the barrels on your right for some bullets. Ignore the ramps and water for now, and follow the passageway to the prison cells. Several Krall will swarm up the stairs - retreat and use the narrow passage to fight them individually, then enter the cell are and push the lever to open the cell door.
Dive into the water beneath the stairwell and swim through the small tunnel to enter a secret room. Enter the water again, swim through the tunnel at the bottom of the shaft. Swim up and you will emerge in a small courtyard. Get the goodies then walk through the doorway near the stairs to reach the courtyard near the main gate. Kill the Skaarj across the courtyard, enter the doorway to the left and take the stairs down. Jump across to the crossbeam ahead, then jump down behind the laser beams to reach the control panel. Approach it to deactivate the laser beams. You’ll find another control panel behind the water-filled tubes in the next room. Push the lever and ride the lift back up.
Now return to the stairway and climb the stairs. Jump down into the Sanctuary and get the Shield Belt near the mirrored wall. Exit the Sanctuary and go out the main gate. Turn right and jump off the cliff into the water below. Climb out of the water onto the landing and kill the Behemoth guarding the Nali. Enter the tunnel on your left and the swim around to the next landing. Three Krall are on patrol, if possible kill them from the water, then walk past the disabled electrodes and step onto the round lift. Jump up to hit the lever for the lift to drop.
Kill the Skaarj in the passage at the bottom and follow the passage. At the end of the passage is a spiral staircase, collect some goodies behind the stairwell then continue upstairs. Deactivate the magnetic locks on the bell tower using the control panel on your left. Enter the small square tunnel and ride the lift up to reach the tower.
Enter the tower door and push the lever inside to activate the lift. At the top of the tower you’ll find Kira and a MiniGun. Pull the switches on either side of the lift to get the Static Discharge Nodes working. Push the lever to ride the lift back down. Jump off on the ledge just above ground level to reach the shipping car. Ride the car to it’s destination, and ride the lift inside to leave the monastery.