First you'll have to solve another anagram (it's on a Coded Scroll in your inventory). Look at the screen below for a solution.
Go down the stairs that are in the corner of the courtyard. You'll find a Silver Coin by the trash in there.
Approach the bulletin board near the church door and open it. There's a Golden Key in there, that will let you open the backyard door to the left.
There's one goon to be stunned before you. Use a shovel.
Somewhere between the boxes among the archways is the Moon Sphere (right screen above)
Move to the other side of the archways and go up the stairs. Wait for the goons to finish talking and try to defeat them one by one. These guys are much tougher than those police geeks you encountered before, so watch out and don't underestimate the power of stealth attack.
There's a Wheelbarrow nearby. You'll find Shears in it. Take it and use it to cut the roses by the fountain. Use the Priory Ring on the engraving there and take the Rough Metal Shard.
You now take control of Langdon, who's apparently been caught and imprisoned. Move the chair by the table in the center of the room to get a Metal Gear. Behind the box on a desk in the corner is a Piece of Cardboard. Move a box near the barrels to the right to grab a Metal Rod.
Now it's time for a most classic adventure game maneuver ever. Use the cardboard on the Gap Under Door and a Metal Rod on the Keyhole. Use the key you just snatched and leave. Sneak on the guard and stun him.
Enter the room opposite your cell. There's Da Vinci's Paddleboat inside. Leave the basement using the door to the right of the TV.
Turn right, towards the main altar. Take care of the one guard in there. To the right of the altar you'll see a cabinet. Take a bandage and another Metal Gear from it. In the opposite corner of the room there's another cabinet, with the next Metal Gear in it.
Wait for the two guards in the back of the church to finish talking, and take them on using Sneak. Enter the room with tombs in it and grab the last Metal Gear from the cabinet there. Go back to the basement and find a Gearbox (go to the left of the TV).
You must place the gears in a way that will let the mechanism function. When you do that (screenshot below), use the lever to the right.
You have to sneak past the two guards so you can enter the trapdoor to the basement. Sneak in the spot shown on the screenshot below and wait for the right moment.
When you're reunited with Langdon, approach the door to the catacombs (screenshot below) and open it.
There's a bandage behind your back - it might be useful. Wait for the guard to get closer and then sneak attack him when he turns away from you. Go forth, doing the same to every other guard you see. In one of the niches to the left you'll see a Templar Seal.
The second seal is in another niche a little bit ahead, behind a cardboard box.
You'll reach a guard and a light switch. Take care of the goon and turn on the light, pressing the 4 buttons in the order shown on the screenshot below.
Use the lever on the left. Enter the room that's been opened and grab a third Templar Seal and a bandage.
Go back the tunnel until you see a respawned guard. Defeat him and find a lever nearby. You'll find yourself in a room with a riddle to be solved. First use your Templar Seals to complete the mechanism on the wall. You now have to turn the seals so they point towards the right directions. Look at the screenshot below.
Head back to the basement level. There are 3 new guards on your way. The first one can be easily wall-attacked (tap the wall to get his attention, look at the left screenshot below to get the idea). As for the other two, try to take at least one of them with sneak attack.
Go to the church and open the main gate in there to find yourself on the courtyard that you started the level on.
By the pillar in the center you'll find a Sharp Metal Shard. Two goons will show themselves, you'll have to fight (certainly a lot of beat-em-up on this level). Go back to the church.
Head to the back part of the church. There's an incomplete shield on the right side - use the two Shards you own on it.
Approach the tomb that says Dark Effigy. You'll have to solve a riddle. The password is RICHARD. Enter this word into the Cryptex.
After a cut-scene, you will have to deal with a long arcade sequence. You are running away from a monk who's chasing you with a gun in his hand. There are doors on your way, and each one requires a different way to get past by. Some of them can be smashed, some require you to use an electrical switch (the combination is the same as earlier) and turn the handle. The last type of gate needs to be lifted up (Langdon apparently doesn't know the word 'crouch'). You'll surely have no problem figuring out which is which. When you reach the end of the corridor, the level will come to an end.