The player starts on the roof of a church, with his back to a large cross and facing a locked bell tower. The key to the tower is held in a workshop room on the other side of the roof.
Head to the door on the right side, and down the stairs. To the right of the hallway is a room with a hidden book terminal (that reveals itself when you approach) and some ammo. To the left is an attic room filled with various crates. At the far end of the attic room is a switch which opens the door at the end of the hallway, revealing a set of stairs.
Go up those stairs to find the workshop area, where you can grab the key that opens the bell tower. Open the bell tower, and jump down. You will find a curved set of stairs leading up to a hallway that heads off to identical rooms at either end. You can go either way down this hall as it all meets up again in a square. The rooms at either end of the hallway contain various monsters and powerups, and are decorate with stained glass windows. You will encounter a stucco textured hallway with two doors and wooden wainscoting. One leads to a small bedroom with fireplace. There is a save terminal behind an obvious wood panel on one side of the room, and a door that leads back to the first hallway on the other. The other door leads to a downward spiral staircase. There is a secret room in this hallway. Look at the top of the wainscoting for a darker area. Tab there to reveal some ammo and a powerup.
Head down the stairs, and enter each door you come to. You will fight various aliens, and find various powerups. Eventually you will come to an office looking area with a desk. The crucifix to the right of the desk is another hidden save terminal. Keep heading down the stairs until you come to a domed area with a statue on a raised platform. To the left is a locked door that needs a key. Straight ahead is a hallway that leads to the cathedral.
Grab the 2x powerup there, and head around the corner to the main cathedral area. If you are running on a slower machine, you may want to pop down to low res to be able to maintain an adequate frame rate to fight the stiff resistance you will find in this area. This is one of the scenario's most CPU challenging portions! Once every thing is dead, pop back into high res to have a look around. I lavished attention on this part of the map, and I would not want you to miss out on it.
At the back of the cathedral are two confessional booths... the key for the locked door is found in the right-hand confessional. More bad guys will show up to hinder your progress when you grab for the key.
There is a secret in this area. If you run diagonally up the stairs you can actually land on the top of the altar, which will cause a door to open briefly to the left as you face down the cathedral. This door can be seen as you face the altar from the main floor of the cathedral... it is lighter than its neighbours up on the wall. To get in this door you have to move fast. From the altar, either jump down and grenade hop up to the door, or for the fleet of foot, hop over to the small ledge and do a side-step run around the pillar to reach the ledge around the corner. This secret area holds a 3x powerup and the SMG.
Once you have the key, head back to the locked door and head down the stairs there. You will enter a small crypt area. As you approach the ammo stash there, an explosion will go off, opening up the wall to the underground portion of the level. Go to this dirt textured area, and perform a series of running hops to get up to the passageway that leads off to the right. Follow this around, hopping across the passageway to the other side, and follow it until you come to the giant head.
Run up to the giant head, and tab on where it's mouth would be. The mouth will drop open to reveal the manuscript you seek. Another explosion will sound, and when you return to the crypt room you will find that the back wall has been blown away to reveal a deeper underground area littered with flaming debris and skeletons. Follow this to the end, where the exit for the level will appear.
The explosions were provided by ticks set to "nuclear hard death" and crushed in triggered platforms. Ticks are great for stuff like that since they die instantly. The "destroyed" room was carefully constructed to look good in both "modes"... complete and destroyed, not an easy task, and some view tricks with overhanging rocks and ledges were pulled to avoid complex views from down in the pit.
The cross at the start of the level is a complete sham built from super thin sky textured polys. I was trying like hell to do a freestanding cross with the Marathon engine.