Full video walkthrough with English commentary!
The fieldwork for A Nun In Trouble will automatically start after progressing the main Vatican quest to the final step. Go to the Sistine Chapel to talk to Gina. after the confession cutscene, we need to head to the Museum. This can be reached by sneaking through the restricted camp next to the Library. There is a hole in the fence between the library and camp entrance. Then, follow Gina through the Museum and collect the clues, including photographing the blood splatters in the next couple rooms.
After the Museum section, we need to meet Gina in Borgia Tower. This can be reached by climbing the scaffolding behind the stage in the main courtyard. Then continue up the tower, taking out the enemies in your way, to save the nun at the top and complete this fieldwork!