In this Chapter Nate has to get to Sam first. Climb out of the window and walk straight ahead. You need to do some climbing but that's it, until you reach an open window.
Climb inside, exit the room and take cover. Wait until the nurse and the priest exit the room. Follow the nurse, stay in cover. In cover, go to the other side of the room and exit again through the open window.
Outside, drop down onto the little white ledge and climb to the left until you can climb up to the roof. Follow the roof, jump over. After the jump, climb on the white ledge to the right, up the rain drain onto the roof. There you interact with the backpack to meet Sam.
Now follow Sam by climbing and jumping, as you did before. You will get to a passage, where you can't follow Sam. Nate will say: "I can't jump that high". Climb to the right and up the shutters to get to Sam. Next tricky bit is the free fall ledge. After Nate drops down, he will glide down the roof. Make sure you make him slide on the left side so Sam can catch him, when you jump.
On the other side, Sam will give you the rope. Use it (R1) to get to the other building. There use the fire ladder to climb down. After a cutscene you'll get a fighting lesson in prison. Fight until the next cutscene.