Note: There are no collectibles in this chapter, so you can enjoy 'freeriding' through the story without having to worry about missing anything.
After the cutscene, hop through the window and make your way over the roof, then turn right. The roof here is too steep to climb over, so climb the nearby power box and proceed via the wall. From here you can make it down the next roof.
Continue left and enter through the open window, then through the nearby door. Take cover at the end of the corridor to overhear the conversation between the nun and the priest. When they're finished conversing, check out Nathan's file in the office to the right, then enter the room in which the nun went (the large doors in the main hall are locked). Take cover behind the white cabinet and the nun will move toward the open window and starts smoking a cigarette. Whenever she's blowing the smoke out of the window, you in turn have a chance to roll to the bench at the right side of the room. The priest will call the nun at this point, allowing you to sneak to the open window.
Drop down a bit and climb to the left, then walk to the end of the roof and climb up via the ledges, moving to the rain pipe to the right. Climb the roof and inspect the flashlight to trigger a cutscene.
At this point, basically all you have to do is follow Sam. At some point you'll reach a big jump. Walk back to the beginning of the roof and run towards the gap and press X at the last moment to make it. Continue following Sam. When you've made it up the steeple, be sure to carefully drop down in the exact middle of the roof (like Sam does), otherwise you end up on a steep roof and slide down a then inevitable death.
At the end, climb up and 'round the building, then to the far left point of the beam and drop down, sliding down the roof and jumping at the last possible instance. Here, simply head down the ladder to conclude this chapter.